diff --git a/api/apps/services/dataset_api_service.py b/api/apps/services/dataset_api_service.py
index 002de87a98..caf002f94d 100644
--- a/api/apps/services/dataset_api_service.py
+++ b/api/apps/services/dataset_api_service.py
@@ -2687,50 +2687,98 @@ async def delete_nav_node(dataset_id: str, tenant_id: str, name: str):
     index_nm, _ = pack
 
     from common.doc_store.doc_store_base import OrderByExpr
+    from rag.advanced_rag.knowlege_compile.dataset_nav import (
+        _LOCK_BLOCKING_TIMEOUT_S,
+        _LOCK_TIMEOUT_S,
+        _nav_lock_key,
+        _remove_dataset_nav_doc_locked,
+    )
+    from rag.utils.redis_conn import RedisDistributedLock
 
-    # Collect the node plus every descendant, level by level via parent_kwd.
-    names: set[str] = {name}
-    frontier: list[str] = [name]
-    for _ in range(64):  # depth guard against a malformed (cyclic) tree
-        if not frontier:
-            break
-        try:
-            res = await thread_pool_exec(
-                settings.docStoreConn.search,
-                ["name"],
-                [],
-                {"compile_kwd": [_NAV_COMPILE_KWD], "parent_kwd": frontier},
-                [],
-                OrderByExpr(),
-                0,
-                10000,
-                index_nm,
-                [dataset_id],
-            )
-            rows = settings.docStoreConn.get_fields(res, ["name"]) or {}
-        except Exception:
-            logging.exception("delete_nav_node: subtree scan failed for kb=%s name=%s", dataset_id, name)
-            break
-        nxt: list[str] = []
-        for row in rows.values():
-            child = row.get("name")
-            if isinstance(child, str) and child and child not in names:
-                names.add(child)
-                nxt.append(child)
-        frontier = nxt
+    async def search_rows(condition):
+        res = await thread_pool_exec(
+            settings.docStoreConn.search,
+            ["id", "name", "type_kwd", "parent_kwd", "doc_id"],
+            [],
+            condition,
+            [],
+            OrderByExpr(),
+            0,
+            10000,
+            index_nm,
+            [dataset_id],
+        )
+        return list((settings.docStoreConn.get_fields(res, ["id", "name", "type_kwd", "parent_kwd", "doc_id"]) or {}).values())
+
+    lock = RedisDistributedLock(
+        _nav_lock_key(dataset_id),
+        timeout=_LOCK_TIMEOUT_S,
+        blocking_timeout=_LOCK_BLOCKING_TIMEOUT_S,
+    )
+    try:
+        await lock.spin_acquire()
+    except Exception:
+        logging.exception("delete_nav_node: lock acquire failed for kb=%s", dataset_id)
+        return False, "Failed to acquire the navigation tree lock."
 
     try:
-        deleted = await thread_pool_exec(
-            settings.docStoreConn.delete,
-            {"compile_kwd": [_NAV_COMPILE_KWD], "name": list(names)},
-            index_nm,
-            dataset_id,
-        )
-    except Exception:
-        logging.exception("delete_nav_node: docStore delete failed for kb=%s name=%s", dataset_id, name)
-        return False, "Failed to delete the navigation node."
+        # ES requires the keyword subfield for exact node-name matching. Infinity
+        # has a scalar varchar name field, while parent_kwd is exact-matchable.
+        name_field = "name.keyword" if settings.DOC_ENGINE.lower() in {"elasticsearch", "opensearch"} else "name"
+        target_condition = {"compile_kwd": [_NAV_COMPILE_KWD], name_field: [name]}
+        rows = await search_rows(target_condition)
+        if not rows and name_field != "name":
+            # Keep this fallback for installations with an older/missing mapping.
+            rows = [row for row in await search_rows({"compile_kwd": [_NAV_COMPILE_KWD]}) if row.get("name") == name]
+        if not rows:
+            return True, {"deleted": 0}
 
-    return True, {"deleted": int(deleted or 0)}
+        # Collect the target and descendants by stable row IDs, not by names.
+        # Names are display values and may collide across malformed/old data.
+        rows_by_id = {row.get("id"): row for row in rows if row.get("id")}
+        frontier = [row.get("name") for row in rows if row.get("name")]
+        for _ in range(64):
+            if not frontier:
+                break
+            children = await search_rows(
+                {"compile_kwd": [_NAV_COMPILE_KWD], "parent_kwd": frontier},
+            )
+            frontier = []
+            for child in children:
+                row_id = child.get("id")
+                child_name = child.get("name")
+                if row_id and row_id not in rows_by_id:
+                    rows_by_id[row_id] = child
+                    if child_name:
+                        frontier.append(child_name)
+
+        deleted = 0
+        # Reuse the existing document-removal path so direct parents are
+        # updated and empty ancestor clusters are cleaned consistently.
+        for row in rows_by_id.values():
+            if row.get("type_kwd") == "nav_doc" and row.get("doc_id"):
+                await _remove_dataset_nav_doc_locked(tenant_id, dataset_id, row["doc_id"])
+                deleted += 1
+
+        cluster_ids = [row_id for row_id, row in rows_by_id.items() if row.get("type_kwd") == "nav_cluster" and row_id]
+        if cluster_ids:
+            deleted_rows = await thread_pool_exec(
+                settings.docStoreConn.delete,
+                {"compile_kwd": [_NAV_COMPILE_KWD], "id": cluster_ids},
+                index_nm,
+                dataset_id,
+            )
+            deleted += int(deleted_rows or 0)
+
+        return True, {"deleted": deleted}
+    except Exception:
+        logging.exception("delete_nav_node: deletion failed for kb=%s name=%s", dataset_id, name)
+        return False, "Failed to delete the navigation node."
+    finally:
+        try:
+            lock.release()
+        except Exception:
+            logging.exception("delete_nav_node: lock release failed for kb=%s", dataset_id)
 
 
 async def update_wiki_page(