diff --git a/gfa_core/extension_stage_lightweight/api.py b/gfa_core/extension_stage_lightweight/api.py
index d57108ac8..11f94800e 100644
--- a/gfa_core/extension_stage_lightweight/api.py
+++ b/gfa_core/extension_stage_lightweight/api.py
@@ -68,7 +68,7 @@ def _server_data_files(value: str | None) -> list[tuple[Path, Path]]:
         if not source.is_dir():
             raise ValueError(f"测试数据路径不是普通文件或目录：{text}")
         files.extend(
-            (item.relative_to(source), item.resolve())
+            (item.relative_to(source.parent), item.resolve())
             for item in sorted(source.rglob("*"))
             if item.is_file()
         )
diff --git a/tests/unit/test_extension_stage_lightweight_api.py b/tests/unit/test_extension_stage_lightweight_api.py
index 5ab656ad7..84cfaf349 100644
--- a/tests/unit/test_extension_stage_lightweight_api.py
+++ b/tests/unit/test_extension_stage_lightweight_api.py
@@ -272,8 +272,32 @@ def test_upload_expands_server_data_directory_preserving_relative_layout(tmp_pat
     assert response.status_code == 202
     assert len(queued) == 1
     staged = tmp_path / "store" / "staging" / "upload-server-directory" / "raw_test_data"
-    assert (staged / "input.fa").is_symlink()
-    assert (staged / "nested" / "model.hmm").is_symlink()
+    assert (staged / "large_case" / "input.fa").is_symlink()
+    assert (staged / "large_case" / "nested" / "model.hmm").is_symlink()
+
+
+def test_upload_server_data_directory_keeps_basename_for_flat_tool_input(tmp_path: Path) -> None:
+    """目录导入保留目录名本身：run.sh 里写死 -f proteomes 时数据必须落在 proteomes/ 下。"""
+    client, queued = _client(tmp_path)
+    source = tmp_path / "proteomes"
+    source.mkdir()
+    (source / "01.col.fa").write_text(">a\nAAAA\n", encoding="utf-8")
+    (source / "02.tibet.fa").write_text(">b\nBBBB\n", encoding="utf-8")
+
+    response = client.post(
+        "/api/lightweight-extension-stages/upload",
+        data={
+            "extension_id": "flat_tool_input",
+            "original_command": "ls proteomes",
+            "operation_token": "upload-flat-tool-input",
+            "raw_data_paths": str(source),
+        },
+    )
+
+    assert response.status_code == 202
+    staged = tmp_path / "store" / "staging" / "upload-flat-tool-input" / "raw_test_data"
+    assert (staged / "proteomes" / "01.col.fa").is_symlink()
+    assert (staged / "proteomes" / "02.tibet.fa").is_symlink()
 
 
 def test_upload_rejects_missing_server_data_path(tmp_path: Path) -> None: