diff --git a/deepmd/pd/train/training.py b/deepmd/pd/train/training.py
index 7d91218468..4daf5c8608 100644
--- a/deepmd/pd/train/training.py
+++ b/deepmd/pd/train/training.py
@@ -81,6 +81,9 @@
 from deepmd.utils.data import (
     DataRequirementItem,
 )
+from deepmd.utils.finetune import (
+    warn_configuration_mismatch_during_finetune,
+)
 from deepmd.utils.path import (
     DPH5Path,
 )
@@ -520,9 +523,8 @@ def get_lr(lr_params: dict[str, Any]) -> BaseLR:
                     new_state_dict = {}
                     target_state_dict = self.wrapper.state_dict()
                     # pretrained_model
-                    pretrained_model = get_model_for_wrapper(
-                        state_dict["_extra_state"]["model_params"]
-                    )
+                    pretrained_model_params = state_dict["_extra_state"]["model_params"]
+                    pretrained_model = get_model_for_wrapper(pretrained_model_params)
                     pretrained_model_wrapper = ModelWrapper(pretrained_model)
                     pretrained_model_wrapper.set_state_dict(state_dict)
                     # update type related params
@@ -557,6 +559,25 @@ def collect_single_finetune_params(
                     ) -> None:
                         _new_fitting = _finetune_rule_single.get_random_fitting()
                         _model_key_from = _finetune_rule_single.get_model_branch()
+                        _input_model_params = (
+                            model_params["model_dict"][_model_key]
+                            if self.multi_task
+                            else model_params
+                        )
+                        _pretrained_model_params = (
+                            pretrained_model_params["model_dict"][_model_key_from]
+                            if "model_dict" in pretrained_model_params
+                            else pretrained_model_params
+                        )
+                        if (
+                            "descriptor" in _input_model_params
+                            and "descriptor" in _pretrained_model_params
+                        ):
+                            warn_configuration_mismatch_during_finetune(
+                                _input_model_params["descriptor"],
+                                _pretrained_model_params["descriptor"],
+                                _model_key_from,
+                            )
                         target_keys = [
                             i
                             for i in _random_state_dict.keys()
diff --git a/deepmd/pd/utils/finetune.py b/deepmd/pd/utils/finetune.py
index 7b3bdf615b..510a91c392 100644
--- a/deepmd/pd/utils/finetune.py
+++ b/deepmd/pd/utils/finetune.py
@@ -8,6 +8,7 @@
 
 from deepmd.utils.finetune import (
     FinetuneRuleItem,
+    warn_descriptor_config_differences,
 )
 
 log = logging.getLogger(__name__)
@@ -57,6 +58,12 @@ def get_finetune_rule_single(
         random_fitting=new_fitting,
     )
     if change_model_params:
+        if "descriptor" in single_config and "descriptor" in single_config_chosen:
+            warn_descriptor_config_differences(
+                single_config["descriptor"],
+                single_config_chosen["descriptor"],
+                model_branch_chosen,
+            )
         trainable_param = {
             "descriptor": single_config.get("descriptor", {}).get("trainable", True),
             "fitting_net": single_config.get("fitting_net", {}).get("trainable", True),
diff --git a/deepmd/pt/train/training.py b/deepmd/pt/train/training.py
index 048ec8b1c6..d5d3965324 100644
--- a/deepmd/pt/train/training.py
+++ b/deepmd/pt/train/training.py
@@ -115,6 +115,9 @@
 from deepmd.utils.data import (
     DataRequirementItem,
 )
+from deepmd.utils.finetune import (
+    warn_configuration_mismatch_during_finetune,
+)
 
 if torch.__version__.startswith("2"):
     import torch._dynamo
@@ -787,9 +790,8 @@ def get_lr(lr_params: dict[str, Any]) -> BaseLR:
                     new_state_dict = {}
                     target_state_dict = self.wrapper.state_dict()
                     # pretrained_model
-                    pretrained_model = get_model_for_wrapper(
-                        state_dict["_extra_state"]["model_params"]
-                    )
+                    pretrained_model_params = state_dict["_extra_state"]["model_params"]
+                    pretrained_model = get_model_for_wrapper(pretrained_model_params)
                     pretrained_model_wrapper = ModelWrapper(pretrained_model)
                     pretrained_model_wrapper.load_state_dict(state_dict)
                     # update type related params
@@ -824,6 +826,25 @@ def collect_single_finetune_params(
                     ) -> None:
                         _new_fitting = _finetune_rule_single.get_random_fitting()
                         _model_key_from = _finetune_rule_single.get_model_branch()
+                        _input_model_params = (
+                            model_params["model_dict"][_model_key]
+                            if self.multi_task
+                            else model_params
+                        )
+                        _pretrained_model_params = (
+                            pretrained_model_params["model_dict"][_model_key_from]
+                            if "model_dict" in pretrained_model_params
+                            else pretrained_model_params
+                        )
+                        if (
+                            "descriptor" in _input_model_params
+                            and "descriptor" in _pretrained_model_params
+                        ):
+                            warn_configuration_mismatch_during_finetune(
+                                _input_model_params["descriptor"],
+                                _pretrained_model_params["descriptor"],
+                                _model_key_from,
+                            )
                         target_keys = [
                             i
                             for i in _random_state_dict.keys()
diff --git a/deepmd/pt/utils/finetune.py b/deepmd/pt/utils/finetune.py
index 0e86c9aa6c..c4db694578 100644
--- a/deepmd/pt/utils/finetune.py
+++ b/deepmd/pt/utils/finetune.py
@@ -14,6 +14,7 @@
 )
 from deepmd.utils.finetune import (
     FinetuneRuleItem,
+    warn_descriptor_config_differences,
 )
 from deepmd.utils.model_branch_dict import (
     get_model_dict,
@@ -69,6 +70,12 @@ def get_finetune_rule_single(
         random_fitting=new_fitting,
     )
     if change_model_params:
+        if "descriptor" in single_config and "descriptor" in single_config_chosen:
+            warn_descriptor_config_differences(
+                single_config["descriptor"],
+                single_config_chosen["descriptor"],
+                model_branch_chosen,
+            )
         trainable_param = {
             "descriptor": single_config.get("descriptor", {}).get("trainable", True),
             "fitting_net": single_config.get("fitting_net", {}).get("trainable", True),
diff --git a/deepmd/pt_expt/train/training.py b/deepmd/pt_expt/train/training.py
index 202c5d10de..bd6fdb02a3 100644
--- a/deepmd/pt_expt/train/training.py
+++ b/deepmd/pt_expt/train/training.py
@@ -70,6 +70,9 @@
 from deepmd.utils.data_system import (
     DeepmdDataSystem,
 )
+from deepmd.utils.finetune import (
+    warn_configuration_mismatch_during_finetune,
+)
 from deepmd.utils.path import (
     DPPath,
 )
@@ -1121,6 +1124,29 @@ def _make_sample(
                             model_with_new_type_stat=model_with_new_type_stat,
                         )
 
+                for model_key in self.model_keys:
+                    finetune_rule = finetune_links[model_key]
+                    _model_key_from = finetune_rule.get_model_branch()
+                    input_model_params = (
+                        model_params["model_dict"][model_key]
+                        if self.multi_task
+                        else model_params
+                    )
+                    branch_pretrained_model_params = (
+                        pretrained_model_params["model_dict"][_model_key_from]
+                        if "model_dict" in pretrained_model_params
+                        else pretrained_model_params
+                    )
+                    if (
+                        "descriptor" in input_model_params
+                        and "descriptor" in branch_pretrained_model_params
+                    ):
+                        warn_configuration_mismatch_during_finetune(
+                            input_model_params["descriptor"],
+                            branch_pretrained_model_params["descriptor"],
+                            _model_key_from,
+                        )
+
                 # Selective weight copy (per-branch key remapping)
                 pretrained_state = pretrained_wrapper.state_dict()
                 target_state = self._unwrapped.state_dict()
diff --git a/deepmd/utils/finetune.py b/deepmd/utils/finetune.py
index c019cc68ab..9bcb85dc82 100644
--- a/deepmd/utils/finetune.py
+++ b/deepmd/utils/finetune.py
@@ -1,8 +1,197 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 import logging
+from collections.abc import (
+    Mapping,
+)
+from copy import (
+    deepcopy,
+)
+from typing import (
+    Any,
+)
 
 log = logging.getLogger(__name__)
 
+_IGNORED_DESCRIPTOR_KEYS = frozenset({"trainable"})
+_MISSING = object()
+_MAX_DESCRIPTOR_CONFIG_DIFFS = 20
+_MAX_CONFIG_VALUE_LENGTH = 200
+
+
+def _infer_synthetic_type_count(descriptor: Mapping[str, Any]) -> int:
+    """Infer a safe type count for descriptor-only normalization.
+
+    The real model ``type_map`` is not available at every finetune warning call
+    site. Use descriptor fields that explicitly encode per-type lists to avoid
+    normalizing a 3+-type descriptor against the historical two-type stub. This
+    is still a best-effort normalization helper: intentional type-map changes
+    may still show up in type-count-dependent fields such as ``sel``.
+    """
+    type_count = 2
+    for key in ("sel", "sel_a", "sel_r"):
+        value = descriptor.get(key)
+        if isinstance(value, list) and all(isinstance(item, int) for item in value):
+            type_count = max(type_count, len(value))
+    exclude_types = descriptor.get("exclude_types")
+    if isinstance(exclude_types, list):
+        for pair in exclude_types:
+            if (
+                isinstance(pair, list)
+                and len(pair) == 2
+                and all(isinstance(item, int) for item in pair)
+            ):
+                type_count = max(type_count, pair[0] + 1, pair[1] + 1)
+    return type_count
+
+
+def _normalize_descriptor_for_compare(
+    descriptor: Mapping[str, Any],
+) -> Mapping[str, Any]:
+    """Normalize a descriptor config so implicit defaults do not warn."""
+    from deepmd.utils.argcheck import (
+        normalize,
+    )
+
+    config = {
+        "model": {
+            "descriptor": deepcopy(dict(descriptor)),
+            "fitting_net": {"neuron": [240, 240, 240]},
+            "type_map": [
+                f"Type{ii}" for ii in range(_infer_synthetic_type_count(descriptor))
+            ],
+        },
+        "training": {"training_data": {"systems": ["fake"]}, "numb_steps": 100},
+    }
+    return normalize(config, multi_task=False)["model"]["descriptor"]
+
+
+def _format_config_value(value: Any) -> str:
+    text = repr(value)
+    if len(text) > _MAX_CONFIG_VALUE_LENGTH:
+        text = text[: _MAX_CONFIG_VALUE_LENGTH - 3] + "..."
+    return text
+
+
+def _iter_descriptor_config_differences(
+    input_config: Any,
+    pretrained_config: Any,
+    prefix: str = "",
+) -> list[tuple[str, Any, Any]]:
+    differences: list[tuple[str, Any, Any]] = []
+    if isinstance(input_config, Mapping) and isinstance(pretrained_config, Mapping):
+        keys = sorted(set(input_config) | set(pretrained_config))
+        for key in keys:
+            if key in _IGNORED_DESCRIPTOR_KEYS:
+                continue
+            key_path = f"{prefix}.{key}" if prefix else str(key)
+            if key not in input_config:
+                differences.append((key_path, _MISSING, pretrained_config[key]))
+            elif key not in pretrained_config:
+                differences.append((key_path, input_config[key], _MISSING))
+            else:
+                differences.extend(
+                    _iter_descriptor_config_differences(
+                        input_config[key], pretrained_config[key], key_path
+                    )
+                )
+        return differences
+    if input_config != pretrained_config:
+        return [(prefix, input_config, pretrained_config)]
+    return differences
+
+
+def _descriptor_config_differences(
+    input_descriptor: Mapping[str, Any],
+    pretrained_descriptor: Mapping[str, Any],
+) -> list[tuple[str, Any, Any]]:
+    """Return meaningful descriptor differences, ignoring implicit defaults."""
+    input_descriptor_cmp: Mapping[str, Any] = input_descriptor
+    pretrained_descriptor_cmp: Mapping[str, Any] = pretrained_descriptor
+    try:
+        input_descriptor_cmp = _normalize_descriptor_for_compare(input_descriptor)
+        pretrained_descriptor_cmp = _normalize_descriptor_for_compare(
+            pretrained_descriptor
+        )
+    except Exception:
+        # Some in-flight or legacy descriptor schemas may not be normalizable with
+        # the minimal synthetic config above. If either side fails, compare raw
+        # descriptor against raw descriptor; mixing normalized and raw values would
+        # report implicit defaults as spurious differences.
+        input_descriptor_cmp = input_descriptor
+        pretrained_descriptor_cmp = pretrained_descriptor
+    return _iter_descriptor_config_differences(
+        input_descriptor_cmp, pretrained_descriptor_cmp
+    )
+
+
+def _format_descriptor_differences(
+    differences: list[tuple[str, Any, Any]],
+    *,
+    overwrite: bool,
+) -> str:
+    lines = []
+    shown = differences[:_MAX_DESCRIPTOR_CONFIG_DIFFS]
+    for key, input_value, pretrained_value in shown:
+        input_text = (
+            "(missing)"
+            if input_value is _MISSING
+            else _format_config_value(input_value)
+        )
+        pretrained_text = (
+            "(missing)"
+            if pretrained_value is _MISSING
+            else _format_config_value(pretrained_value)
+        )
+        if overwrite:
+            lines.append(f"  {key}: {input_text} -> {pretrained_text}")
+        else:
+            lines.append(f"  {key}: input={input_text}, pretrained={pretrained_text}")
+    remaining = len(differences) - len(shown)
+    if remaining > 0:
+        lines.append(f"  ... and {remaining} more difference(s)")
+    return "\n".join(lines)
+
+
+def warn_descriptor_config_differences(
+    input_descriptor: Mapping[str, Any],
+    pretrained_descriptor: Mapping[str, Any],
+    model_branch: str = "Default",
+) -> None:
+    """Warn when ``--use-pretrain-script`` overwrites descriptor config."""
+    differences = _descriptor_config_differences(
+        input_descriptor, pretrained_descriptor
+    )
+    if not differences:
+        return
+    log.warning(
+        "Descriptor configuration in input.json differs from pretrained model "
+        f"(branch '{model_branch}'). The input descriptor configuration will be "
+        "overwritten with the pretrained model's descriptor configuration "
+        "except for the trainable flag:\n"
+        + _format_descriptor_differences(differences, overwrite=True)
+    )
+
+
+def warn_configuration_mismatch_during_finetune(
+    input_descriptor: Mapping[str, Any],
+    pretrained_descriptor: Mapping[str, Any],
+    model_branch: str = "Default",
+) -> None:
+    """Warn when fine-tuning loads only compatible descriptor parameters."""
+    differences = _descriptor_config_differences(
+        input_descriptor, pretrained_descriptor
+    )
+    if not differences:
+        return
+    log.warning(
+        "Descriptor configuration mismatch detected between input.json and "
+        f"pretrained model (branch '{model_branch}'). Only descriptor parameters "
+        "that are compatible with the pretrained model can be reused; "
+        "incompatible parameters may be reinitialized, skipped, or rejected by "
+        "backend-specific loading:\n"
+        + _format_descriptor_differences(differences, overwrite=False)
+    )
+
 
 class FinetuneRuleItem:
     def __init__(
diff --git a/source/tests/common/test_finetune_utils.py b/source/tests/common/test_finetune_utils.py
new file mode 100644
index 0000000000..776d7bb131
--- /dev/null
+++ b/source/tests/common/test_finetune_utils.py
@@ -0,0 +1,99 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+import logging
+
+from deepmd.utils import (
+    finetune,
+)
+
+
+def test_descriptor_normalization_uses_descriptor_type_count():
+    assert finetune._infer_synthetic_type_count({"sel": [16, 24, 32]}) == 3
+    assert finetune._infer_synthetic_type_count({"exclude_types": [[0, 3]]}) == 4
+
+
+def test_descriptor_config_warning_reports_nested_difference(monkeypatch, caplog):
+    monkeypatch.setattr(
+        finetune,
+        "_normalize_descriptor_for_compare",
+        lambda descriptor: descriptor,
+    )
+
+    input_descriptor = {
+        "type": "dpa3",
+        "repflow": {"nlayers": 6, "rcut": 6.0},
+        "trainable": False,
+    }
+    pretrained_descriptor = {
+        "type": "dpa3",
+        "repflow": {"nlayers": 16, "rcut": 6.0},
+        "trainable": True,
+    }
+
+    with caplog.at_level(logging.WARNING):
+        finetune.warn_configuration_mismatch_during_finetune(
+            input_descriptor,
+            pretrained_descriptor,
+        )
+
+    assert "repflow.nlayers" in caplog.text
+    assert "input=6, pretrained=16" in caplog.text
+    assert "trainable" not in caplog.text
+
+
+def test_descriptor_config_warning_skips_default_only_difference(caplog):
+    with caplog.at_level(logging.WARNING):
+        finetune.warn_descriptor_config_differences(
+            {"type": "se_e2_a", "sel": [16, 16], "rcut": 6.0},
+            {
+                "type": "se_e2_a",
+                "sel": [16, 16],
+                "rcut": 6.0,
+                "activation_function": "tanh",
+            },
+        )
+
+    assert caplog.text == ""
+
+
+def test_descriptor_config_warning_falls_back_to_raw_if_normalization_fails(
+    monkeypatch, caplog
+):
+    input_descriptor = {"type": "dpa3", "repflow": {"nlayers": 6}}
+    pretrained_descriptor = {"type": "dpa3", "repflow": {"nlayers": 16}}
+
+    def normalize_one_side_then_fail(descriptor):
+        if descriptor is pretrained_descriptor:
+            raise ValueError("legacy schema")
+        return {**descriptor, "implicit_default": True}
+
+    monkeypatch.setattr(
+        finetune,
+        "_normalize_descriptor_for_compare",
+        normalize_one_side_then_fail,
+    )
+
+    with caplog.at_level(logging.WARNING):
+        finetune.warn_configuration_mismatch_during_finetune(
+            input_descriptor,
+            pretrained_descriptor,
+        )
+
+    assert "repflow.nlayers" in caplog.text
+    assert "implicit_default" not in caplog.text
+
+
+def test_descriptor_config_warning_distinguishes_none_from_missing(monkeypatch, caplog):
+    monkeypatch.setattr(
+        finetune,
+        "_normalize_descriptor_for_compare",
+        lambda descriptor: descriptor,
+    )
+
+    with caplog.at_level(logging.WARNING):
+        finetune.warn_configuration_mismatch_during_finetune(
+            {"type": "dpa3", "input_none": None},
+            {"type": "dpa3", "pretrained_none": None},
+        )
+
+    assert "input_none: input=None, pretrained=(missing)" in caplog.text
+    assert "pretrained_none: input=(missing), pretrained=None" in caplog.text