diff --git a/openviking/retrieve/hierarchical_retriever.py b/openviking/retrieve/hierarchical_retriever.py
index 62782bf36..1306870c0 100644
--- a/openviking/retrieve/hierarchical_retriever.py
+++ b/openviking/retrieve/hierarchical_retriever.py
@@ -273,26 +273,32 @@ def _rerank_scores(
         if not self._rerank_client or not documents:
             return fallback_scores
 
+        rerank_documents = [
+            (index, document) for index, document in enumerate(documents) if document.strip()
+        ]
+        if not rerank_documents:
+            return fallback_scores
+
         try:
-            scores = self._rerank_client.rerank_batch(query, documents)
+            scores = self._rerank_client.rerank_batch(
+                query, [document for _, document in rerank_documents]
+            )
         except Exception as e:
             logger.warning(
                 "[HierarchicalRetriever] Rerank failed, fallback to vector scores: %s", e
             )
             return fallback_scores
 
-        if not scores or len(scores) != len(documents):
+        if not scores or len(scores) != len(rerank_documents):
             logger.warning(
                 "[HierarchicalRetriever] Invalid rerank result, fallback to vector scores"
             )
             return fallback_scores
 
-        normalized_scores: List[float] = []
-        for score, fallback in zip(scores, fallback_scores, strict=True):
+        normalized_scores = list(fallback_scores)
+        for score, (index, _) in zip(scores, rerank_documents, strict=True):
             if isinstance(score, (int, float)):
-                normalized_scores.append(float(score))
-            else:
-                normalized_scores.append(fallback)
+                normalized_scores[index] = float(score)
         return normalized_scores
 
     def _merge_starting_points(
diff --git a/tests/retrieve/test_hierarchical_retriever_rerank.py b/tests/retrieve/test_hierarchical_retriever_rerank.py
index 1c5ab89de..2b1e4c5d8 100644
--- a/tests/retrieve/test_hierarchical_retriever_rerank.py
+++ b/tests/retrieve/test_hierarchical_retriever_rerank.py
@@ -300,6 +300,29 @@ def test_merge_starting_points_prefers_rerank_scores_in_thinking_mode(monkeypatc
     assert fake_client.calls == [("hello", ["root A", "root B"])]
 
 
+def test_rerank_scores_preserves_fallbacks_for_empty_documents(monkeypatch):
+    fake_client = FakeRerankClient([0.95, 0.05])
+    monkeypatch.setattr(
+        "openviking.retrieve.hierarchical_retriever.RerankClient.from_config",
+        lambda config: fake_client,
+    )
+
+    retriever = HierarchicalRetriever(
+        storage=DummyStorage(),
+        embedder=DummyEmbedder(),
+        rerank_config=_config(),
+    )
+
+    scores = retriever._rerank_scores(
+        "hello",
+        ["root A", "", "   ", "root D"],
+        [0.2, 0.8, 0.7, 0.4],
+    )
+
+    assert scores == [0.95, 0.8, 0.7, 0.05]
+    assert fake_client.calls == [("hello", ["root A", "root D"])]
+
+
 @pytest.mark.asyncio
 async def test_retrieve_uses_rerank_scores_in_thinking_mode(monkeypatch):
     fake_client = FakeRerankClient([0.95, 0.05, 0.11, 0.95])