diff --git a/deepmd/jax/train/trainer.py b/deepmd/jax/train/trainer.py
index c77bc944b5..fec5e15628 100644
--- a/deepmd/jax/train/trainer.py
+++ b/deepmd/jax/train/trainer.py
@@ -806,8 +806,14 @@ def _save_checkpoint(self, step: int) -> None:
         log.info(f"Trained model has been saved to: {ckpt_path!s}")
         _link_checkpoint(ckpt_path, Path(f"{self.save_ckpt}.jax"))
         self._cleanup_old_checkpoints()
-        with open("checkpoint", "w") as fp:
-            fp.write(f"{self.save_ckpt}.jax")
+        # Write the pointer next to the checkpoint prefix, with a value relative
+        # to that directory (basename only). The freeze entrypoint looks for the
+        # pointer inside the folder it is given and resolves the value relative
+        # to it, so a directory-valued save_ckpt would otherwise be unresolvable.
+        ckpt_dir = Path(self.save_ckpt).parent
+        ckpt_dir.mkdir(parents=True, exist_ok=True)
+        with open(ckpt_dir / "checkpoint", "w") as fp:
+            fp.write(f"{Path(self.save_ckpt).name}.jax")
 
     def _save_full_validation_checkpoint(
         self,
diff --git a/source/tests/jax/test_checkpoint_pointer.py b/source/tests/jax/test_checkpoint_pointer.py
new file mode 100644
index 0000000000..8f2faf44b6
--- /dev/null
+++ b/source/tests/jax/test_checkpoint_pointer.py
@@ -0,0 +1,65 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+"""Test the JAX trainer writes its checkpoint pointer beside save_ckpt.
+
+JAX training writes checkpoint directories and the stable ``.jax`` link relative
+to ``save_ckpt`` (which may include a directory), but used to always write the
+``checkpoint`` pointer file to the current working directory with a value that
+still carried the directory prefix. The freeze entrypoint expects the pointer
+inside the folder it is given and resolves its value relative to that folder, so
+a directory-valued ``save_ckpt`` broke freeze/restart tooling.
+"""
+
+import os
+import tempfile
+import unittest
+from pathlib import (
+    Path,
+)
+from unittest import (
+    mock,
+)
+
+from deepmd.jax.train.trainer import (
+    DPTrainer,
+)
+
+
+class TestCheckpointPointer(unittest.TestCase):
+    def setUp(self) -> None:
+        self.tmpdir = tempfile.TemporaryDirectory()
+        self.cwd = os.getcwd()
+        os.chdir(self.tmpdir.name)
+
+    def tearDown(self) -> None:
+        os.chdir(self.cwd)
+        self.tmpdir.cleanup()
+
+    def _save(self, save_ckpt: str) -> None:
+        trainer = DPTrainer.__new__(DPTrainer)
+        trainer.save_ckpt = save_ckpt
+        with (
+            mock.patch.object(DPTrainer, "_write_checkpoint"),
+            mock.patch.object(DPTrainer, "_cleanup_old_checkpoints"),
+            mock.patch("deepmd.jax.train.trainer._link_checkpoint"),
+        ):
+            trainer._save_checkpoint(1)
+
+    def test_pointer_beside_ckpt_for_subdir(self) -> None:
+        # save_ckpt with a directory: pointer must land in that directory with a
+        # value relative to it (basename only), so freeze(subdir) resolves it.
+        self._save("subdir/model.ckpt")
+        pointer = Path("subdir") / "checkpoint"
+        self.assertTrue(pointer.is_file())
+        self.assertEqual(pointer.read_text(), "model.ckpt.jax")
+        self.assertFalse(Path("checkpoint").exists())
+
+    def test_pointer_in_cwd_for_bare_name(self) -> None:
+        # default/bare save_ckpt: pointer stays in the CWD (parent is ".").
+        self._save("model.ckpt")
+        pointer = Path("checkpoint")
+        self.assertTrue(pointer.is_file())
+        self.assertEqual(pointer.read_text(), "model.ckpt.jax")
+
+
+if __name__ == "__main__":
+    unittest.main()