diff --git a/internal/datacoord/handler.go b/internal/datacoord/handler.go
index 505820e970..7f7bf15046 100644
--- a/internal/datacoord/handler.go
+++ b/internal/datacoord/handler.go
@@ -145,25 +145,52 @@ func (h *ServerHandler) GetQueryVChanPositions(channel *channel, partitionIDs ..
 			unIndexedIDs.Insert(s.GetID())
 		}
 	}
-	hasUnIndexed := true
-	for hasUnIndexed {
-		hasUnIndexed = false
-		for id := range unIndexedIDs {
-			// Indexed segments are compacted to a raw segment,
-			// replace it with the indexed ones
-			if len(segmentInfos[id].GetCompactionFrom()) > 0 {
-				unIndexedIDs.Remove(id)
-				for _, segID := range segmentInfos[id].GetCompactionFrom() {
-					if indexed.Contain(segID) {
-						indexedIDs.Insert(segID)
-					} else {
-						unIndexedIDs.Insert(segID)
-						hasUnIndexed = true
-					}
-				}
-				droppedIDs.Remove(segmentInfos[id].GetCompactionFrom()...)
+	// ================================================
+	// Segments blood relationship:
+	//          a   b
+	//           \ /
+	//            c   d
+	//             \ /
+	//              e
+	//
+	// GC:        a, b
+	// Indexed:   c, d, e
+	//              ||
+	//              || (Index dropped and creating new index and not finished)
+	//              \/
+	// UnIndexed: c, d, e
+	//
+	// Retrieve unIndexed expected result:
+	// unIndexed: c, d
+	// ================================================
+	isValid := func(ids ...UniqueID) bool {
+		for _, id := range ids {
+			if seg, ok := segmentInfos[id]; !ok || seg == nil {
+				return false
 			}
 		}
+		return true
+	}
+	retrieveUnIndexed := func() bool {
+		continueRetrieve := false
+		for id := range unIndexedIDs {
+			compactionFrom := segmentInfos[id].GetCompactionFrom()
+			if len(compactionFrom) > 0 && isValid(compactionFrom...) {
+				for _, fromID := range compactionFrom {
+					if indexed.Contain(fromID) {
+						indexedIDs.Insert(fromID)
+					} else {
+						unIndexedIDs.Insert(fromID)
+						continueRetrieve = true
+					}
+				}
+				unIndexedIDs.Remove(id)
+				droppedIDs.Remove(compactionFrom...)
+			}
+		}
+		return continueRetrieve
+	}
+	for retrieveUnIndexed() {
 	}
 
 	return &datapb.VchannelInfo{
diff --git a/internal/datacoord/server_test.go b/internal/datacoord/server_test.go
index 111b253143..dd2fcecf72 100644
--- a/internal/datacoord/server_test.go
+++ b/internal/datacoord/server_test.go
@@ -2371,6 +2371,253 @@ func TestGetQueryVChanPositions(t *testing.T) {
 	})
 }
 
+func TestGetQueryVChanPositions_Retrieve_unIndexed(t *testing.T) {
+	t.Run("ab GC-ed, cde unIndexed", func(t *testing.T) {
+		svr := newTestServer(t, nil)
+		defer closeTestServer(t, svr)
+		schema := newTestSchema()
+		svr.meta.AddCollection(&collectionInfo{
+			ID:     0,
+			Schema: schema,
+		})
+		err := svr.meta.CreateIndex(&model.Index{
+			TenantID:     "",
+			CollectionID: 0,
+			FieldID:      2,
+			IndexID:      1,
+		})
+		assert.Nil(t, err)
+		c := &datapb.SegmentInfo{
+			ID:            1,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Dropped,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+			CompactionFrom: []int64{99, 100}, // a, b which have been GC-ed
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(c))
+		assert.Nil(t, err)
+		d := &datapb.SegmentInfo{
+			ID:            2,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Dropped,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(d))
+		assert.Nil(t, err)
+		e := &datapb.SegmentInfo{
+			ID:            3,
+			CollectionID:  0,
+			PartitionID:   1,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Flushed,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+			CompactionFrom: []int64{1, 2}, // c, d
+		}
+
+		err = svr.meta.AddSegment(NewSegmentInfo(e))
+		assert.Nil(t, err)
+		vchan := svr.handler.GetQueryVChanPositions(&channel{Name: "ch1", CollectionID: 0}, allPartitionID)
+		assert.EqualValues(t, 0, len(vchan.FlushedSegmentIds))
+		assert.EqualValues(t, 2, len(vchan.UnflushedSegmentIds))
+		assert.ElementsMatch(t, []int64{c.GetID(), d.GetID()}, vchan.UnflushedSegmentIds) // expected c, d
+	})
+
+	t.Run("a GC-ed, bcde unIndexed", func(t *testing.T) {
+		svr := newTestServer(t, nil)
+		defer closeTestServer(t, svr)
+		schema := newTestSchema()
+		svr.meta.AddCollection(&collectionInfo{
+			ID:     0,
+			Schema: schema,
+		})
+		err := svr.meta.CreateIndex(&model.Index{
+			TenantID:     "",
+			CollectionID: 0,
+			FieldID:      2,
+			IndexID:      1,
+		})
+		assert.Nil(t, err)
+		a := &datapb.SegmentInfo{
+			ID:            99,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Dropped,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(a))
+		assert.Nil(t, err)
+
+		c := &datapb.SegmentInfo{
+			ID:            1,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Dropped,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+			CompactionFrom: []int64{99, 100}, // a, b which have been GC-ed
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(c))
+		assert.Nil(t, err)
+		d := &datapb.SegmentInfo{
+			ID:            2,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Dropped,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(d))
+		assert.Nil(t, err)
+		e := &datapb.SegmentInfo{
+			ID:            3,
+			CollectionID:  0,
+			PartitionID:   1,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Flushed,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+			CompactionFrom: []int64{1, 2}, // c, d
+		}
+
+		err = svr.meta.AddSegment(NewSegmentInfo(e))
+		assert.Nil(t, err)
+		vchan := svr.handler.GetQueryVChanPositions(&channel{Name: "ch1", CollectionID: 0}, allPartitionID)
+		assert.EqualValues(t, 0, len(vchan.FlushedSegmentIds))
+		assert.EqualValues(t, 2, len(vchan.UnflushedSegmentIds))
+		assert.ElementsMatch(t, []int64{c.GetID(), d.GetID()}, vchan.UnflushedSegmentIds) // expected c, d
+	})
+
+	t.Run("ab GC-ed, c unIndexed, de indexed", func(t *testing.T) {
+		svr := newTestServer(t, nil)
+		defer closeTestServer(t, svr)
+		schema := newTestSchema()
+		svr.meta.AddCollection(&collectionInfo{
+			ID:     0,
+			Schema: schema,
+		})
+		err := svr.meta.CreateIndex(&model.Index{
+			TenantID:     "",
+			CollectionID: 0,
+			FieldID:      2,
+			IndexID:      1,
+		})
+		assert.Nil(t, err)
+		c := &datapb.SegmentInfo{
+			ID:            1,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Dropped,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+			CompactionFrom: []int64{99, 100}, // a, b which have been GC-ed
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(c))
+		assert.Nil(t, err)
+		d := &datapb.SegmentInfo{
+			ID:            2,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Dropped,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(d))
+		assert.Nil(t, err)
+		err = svr.meta.AddSegmentIndex(&model.SegmentIndex{
+			SegmentID: 2,
+			BuildID:   1,
+			IndexID:   1,
+		})
+		assert.Nil(t, err)
+		err = svr.meta.FinishTask(&indexpb.IndexTaskInfo{
+			BuildID: 1,
+			State:   commonpb.IndexState_Finished,
+		})
+		assert.Nil(t, err)
+		e := &datapb.SegmentInfo{
+			ID:            3,
+			CollectionID:  0,
+			PartitionID:   0,
+			InsertChannel: "ch1",
+			State:         commonpb.SegmentState_Flushed,
+			DmlPosition: &msgpb.MsgPosition{
+				ChannelName: "ch1",
+				MsgID:       []byte{1, 2, 3},
+				MsgGroup:    "",
+				Timestamp:   1,
+			},
+			CompactionFrom: []int64{1, 2}, // c, d
+		}
+		err = svr.meta.AddSegment(NewSegmentInfo(e))
+		assert.Nil(t, err)
+		err = svr.meta.AddSegmentIndex(&model.SegmentIndex{
+			SegmentID: 3,
+			BuildID:   2,
+			IndexID:   1,
+		})
+		assert.Nil(t, err)
+		err = svr.meta.FinishTask(&indexpb.IndexTaskInfo{
+			BuildID: 2,
+			State:   commonpb.IndexState_Finished,
+		})
+		assert.Nil(t, err)
+
+		vchan := svr.handler.GetQueryVChanPositions(&channel{Name: "ch1", CollectionID: 0}, allPartitionID)
+		assert.EqualValues(t, 1, len(vchan.FlushedSegmentIds))
+		assert.EqualValues(t, 0, len(vchan.UnflushedSegmentIds))
+		assert.ElementsMatch(t, []int64{e.GetID()}, vchan.FlushedSegmentIds) // expected e
+	})
+}
+
 func TestShouldDropChannel(t *testing.T) {
 	type myRootCoord struct {
 		mocks.RootCoord