diff --git a/lib/mergeset/block_stream_writer.go b/lib/mergeset/block_stream_writer.go
index 8341b8318..a184d7a4b 100644
--- a/lib/mergeset/block_stream_writer.go
+++ b/lib/mergeset/block_stream_writer.go
@@ -148,12 +148,15 @@ func (bsw *blockStreamWriter) WriteBlock(ib *inmemoryBlock) {
 	bsw.lensBlockOffset += uint64(bsw.bh.lensBlockSize)
 
 	// Write blockHeader
+	unpackedIndexBlockBufLen := len(bsw.unpackedIndexBlockBuf)
 	bsw.unpackedIndexBlockBuf = bsw.bh.Marshal(bsw.unpackedIndexBlockBuf)
+	if len(bsw.unpackedIndexBlockBuf) > maxIndexBlockSize {
+		bsw.unpackedIndexBlockBuf = bsw.unpackedIndexBlockBuf[:unpackedIndexBlockBufLen]
+		bsw.flushIndexData()
+		bsw.unpackedIndexBlockBuf = bsw.bh.Marshal(bsw.unpackedIndexBlockBuf)
+	}
 	bsw.bh.Reset()
 	bsw.mr.blockHeadersCount++
-	if len(bsw.unpackedIndexBlockBuf) >= maxIndexBlockSize {
-		bsw.flushIndexData()
-	}
 }
 
 // The maximum size of index block with multiple blockHeaders.
diff --git a/lib/storage/block_stream_writer.go b/lib/storage/block_stream_writer.go
index 0029534e7..9d90c7741 100644
--- a/lib/storage/block_stream_writer.go
+++ b/lib/storage/block_stream_writer.go
@@ -143,11 +143,14 @@ func (bsw *blockStreamWriter) WriteExternalBlock(b *Block, ph *partHeader, rowsM
 		atomic.AddUint64(&timestampsBlocksMerged, 1)
 		atomic.AddUint64(&timestampsBytesSaved, uint64(len(timestampsData)))
 	}
+	indexDataLen := len(bsw.indexData)
 	bsw.indexData = append(bsw.indexData, headerData...)
-	bsw.mr.RegisterBlockHeader(&b.bh)
-	if len(bsw.indexData) >= maxBlockSize {
+	if len(bsw.indexData) > maxBlockSize {
+		bsw.indexData = bsw.indexData[:indexDataLen]
 		bsw.flushIndexData()
+		bsw.indexData = append(bsw.indexData, headerData...)
 	}
+	bsw.mr.RegisterBlockHeader(&b.bh)
 	if !usePrevTimestamps {
 		bsw.prevTimestampsData = append(bsw.prevTimestampsData[:0], timestampsData...)
 		bsw.prevTimestampsBlockOffset = bsw.timestampsBlockOffset