diff --git a/src/backend/job/biz-job/src/main/kotlin/com/tencent/bkrepo/job/batch/DeletedNodeCleanupJob.kt b/src/backend/job/biz-job/src/main/kotlin/com/tencent/bkrepo/job/batch/DeletedNodeCleanupJob.kt
index 1f94b5c6ad..a1fe31dd59 100644
--- a/src/backend/job/biz-job/src/main/kotlin/com/tencent/bkrepo/job/batch/DeletedNodeCleanupJob.kt
+++ b/src/backend/job/biz-job/src/main/kotlin/com/tencent/bkrepo/job/batch/DeletedNodeCleanupJob.kt
@@ -27,6 +27,7 @@
 
 package com.tencent.bkrepo.job.batch
 
+import com.mongodb.client.result.DeleteResult
 import com.tencent.bkrepo.common.mongo.constant.ID
 import com.tencent.bkrepo.common.service.cluster.ClusterProperties
 import com.tencent.bkrepo.fs.server.constant.FAKE_SHA256
@@ -44,9 +45,12 @@ import org.slf4j.LoggerFactory
 import org.springframework.boot.context.properties.EnableConfigurationProperties
 import org.springframework.data.domain.PageRequest
 import org.springframework.data.mongodb.core.MongoTemplate
+import org.springframework.data.mongodb.core.findOne
 import org.springframework.data.mongodb.core.query.Criteria
 import org.springframework.data.mongodb.core.query.Query
+import org.springframework.data.mongodb.core.query.Update
 import org.springframework.data.mongodb.core.query.and
+import org.springframework.data.mongodb.core.query.inValues
 import org.springframework.data.mongodb.core.query.isEqualTo
 import org.springframework.data.mongodb.core.query.where
 import org.springframework.stereotype.Component
@@ -83,6 +87,12 @@ class DeletedNodeCleanupJob(
         val deleted: LocalDateTime?
     )
 
+    data class FileReference(
+        val sha256: String,
+        val credentialsKey: String,
+        val count: String
+    )
+
     override fun getLockAtMostFor(): Duration = Duration.ofDays(7)
 
     override fun createJobContext(): DeletedNodeCleanupJobContext {
@@ -121,14 +131,10 @@ class DeletedNodeCleanupJob(
             val deletedNodeList =
                 mongoTemplate.find(query, Node::class.java, nodeCollectionName).takeIf { it.isNotEmpty() } ?: break
             logger.info("Retrieved [${deletedNodeList.size}] deleted records from ${row.projectId}/${row.name}")
-            deletedNodeList.forEach { node ->
-                cleanUpNode(row, node, nodeCollectionName)
-                if (node.folder) {
-                    context.folderCount.incrementAndGet()
-                } else {
-                    context.fileCount.incrementAndGet()
-                }
-            }
+            val folderNodeList = deletedNodeList.filter { it.folder }
+            cleanupFolderNode(context, folderNodeList, nodeCollectionName)
+            val fileNodeList = deletedNodeList.filter { !it.folder }
+            cleanUpFileNode(context, row, fileNodeList, nodeCollectionName)
         }
         // 仓库被标记为已删除，且该仓库下不存在任何节点时，删除仓库
         if (row.deleted != null &&
@@ -141,24 +147,76 @@ class DeletedNodeCleanupJob(
         }
     }
 
-    private fun cleanUpNode(repo: Repository, node: Node, nodeCollectionName: String) {
-        var fileReferenceChanged = false
+    private fun cleanupFolderNode(
+        context: DeletedNodeCleanupJobContext,
+        nodes: List<Node>,
+        nodeCollectionName: String
+    ) {
+        val idList = nodes.map { it.id }
+        val query = Query.query(Criteria.where(ID).inValues(idList))
+        val result = mongoTemplate.remove(query, nodeCollectionName)
+        context.folderCount.addAndGet(result.deletedCount)
+    }
+
+    private fun cleanUpFileNode(
+        context: DeletedNodeCleanupJobContext,
+        repo: Repository,
+        nodes: List<Node>,
+        nodeCollectionName: String
+    ) {
+        val idList = nodes.filter { it.clusterNames == null || it.clusterNames.contains(clusterProperties.self.name) }
+            .map { it.id }
+        val query = Query.query(Criteria.where(ID).inValues(idList))
+        val sha256List = nodes.filter { !it.sha256.isNullOrBlank() && it.sha256 != FAKE_SHA256 }
+            .map { it.sha256!! }.distinct()
+
+        var result: DeleteResult? = null
         try {
-            val nodeQuery = Query.query(Criteria.where(ID).isEqualTo(node.id))
-            mongoTemplate.remove(nodeQuery, nodeCollectionName)
-            if (!node.folder
-                && (node.clusterNames == null || node.clusterNames.contains(clusterProperties.self.name))
-            ) {
-                fileReferenceChanged = decrementFileReference(node, repo)
-            }
+            result = mongoTemplate.remove(query, nodeCollectionName)
+            decrementFileReferences(sha256List, repo.credentialsKey)
         } catch (ignored: Exception) {
-            logger.error("Clean up deleted node[$node] failed in collection[$nodeCollectionName].", ignored)
-            if (fileReferenceChanged) {
-                incrementFileReference(node, repo)
+            logger.error("Clean up deleted nodes[$idList] failed in collection[$nodeCollectionName].", ignored)
+        }
+
+        context.fileCount.addAndGet(result?.deletedCount ?: 0)
+    }
+
+    private fun decrementFileReferences(sha256List: List<String>, credentialsKey: String?) {
+        sha256List.forEach {
+            val collectionName = COLLECTION_FILE_REFERENCE + MongoShardingUtils.shardingSequence(it, SHARDING_COUNT)
+            val criteria = buildCriteria(it, credentialsKey)
+            criteria.and(FileReference::count.name).gt(0)
+            val query = Query(criteria)
+            val update = Update().apply { inc(FileReference::count.name, -1) }
+            val result = mongoTemplate.updateFirst(query, update, collectionName)
+
+            if (result.modifiedCount == 1L) {
+                logger.info("Decrement references of file [$it] on credentialsKey [$credentialsKey].")
+                return@forEach
+            }
+
+            val newQuery = Query(buildCriteria(it, credentialsKey))
+            mongoTemplate.findOne<FileReference>(newQuery, collectionName) ?: run {
+                logger.error("Failed to decrement reference of file [$it] on credentialsKey [$credentialsKey]")
+                return@forEach
             }
+
+            logger.error(
+                "Failed to decrement reference of file [$it] on credentialsKey [$credentialsKey]: " +
+                    "reference count is 0."
+            )
         }
     }
 
+    private fun buildCriteria(
+        it: String,
+        credentialsKey: String?
+    ): Criteria {
+        val criteria = Criteria.where(FileReference::sha256.name).`is`(it)
+        criteria.and(FileReference::credentialsKey.name).`is`(credentialsKey)
+        return criteria
+    }
+
     private fun buildNodeQuery(projectId: String, repoName: String, deletedBefore: LocalDateTime? = null): Query {
         val criteria = where(Node::projectId).isEqualTo(projectId)
             .and(Node::repoName).isEqualTo(repoName)
@@ -183,6 +241,7 @@ class DeletedNodeCleanupJob(
     companion object {
         private val logger = LoggerFactory.getLogger(DeletedNodeCleanupJob::class.java)
         private const val COLLECTION_NODE_PREFIX = "node_"
+        private const val COLLECTION_FILE_REFERENCE = "file_reference_"
         private const val COLLECTION_REPOSITORY = "repository"
         private const val PAGE_SIZE = 1000
     }
diff --git a/src/backend/repository/biz-repository/src/main/kotlin/com/tencent/bkrepo/repository/service/file/impl/FileReferenceServiceImpl.kt b/src/backend/repository/biz-repository/src/main/kotlin/com/tencent/bkrepo/repository/service/file/impl/FileReferenceServiceImpl.kt
index 821dc9953e..2df53820ab 100644
--- a/src/backend/repository/biz-repository/src/main/kotlin/com/tencent/bkrepo/repository/service/file/impl/FileReferenceServiceImpl.kt
+++ b/src/backend/repository/biz-repository/src/main/kotlin/com/tencent/bkrepo/repository/service/file/impl/FileReferenceServiceImpl.kt
@@ -92,24 +92,28 @@ class FileReferenceServiceImpl(
     }
 
     override fun decrement(sha256: String, credentialsKey: String?): Boolean {
-        val query = buildQuery(sha256, credentialsKey)
-        val fileReference = fileReferenceDao.findOne(query) ?: run {
+        val criteria = Criteria.where(TFileReference::sha256.name).`is`(sha256)
+        criteria.and(TFileReference::credentialsKey.name).`is`(credentialsKey)
+        criteria.and(TFileReference::count.name).gt(0)
+        val query = Query(criteria)
+        val update = Update().apply { inc(TFileReference::count.name, -1) }
+        val result = fileReferenceDao.updateFirst(query, update)
+
+        if (result.modifiedCount == 1L) {
+            logger.info("Decrement references of file [$sha256] on credentialsKey [$credentialsKey].")
+            return true
+        }
+
+        fileReferenceDao.findOne(buildQuery(sha256, credentialsKey)) ?: run {
             logger.error("Failed to decrement reference of file [$sha256] on credentialsKey [$credentialsKey]")
             return false
         }
 
-        return if (fileReference.count >= 1) {
-            val update = Update().apply { inc(TFileReference::count.name, -1) }
-            fileReferenceDao.upsert(query, update)
-            logger.info("Decrement references of file [$sha256] on credentialsKey [$credentialsKey].")
-            true
-        } else {
-            logger.error(
-                "Failed to decrement reference of file [$sha256] on credentialsKey [$credentialsKey]: " +
-                    "reference count is 0."
-            )
-            false
-        }
+        logger.error(
+            "Failed to decrement reference of file [$sha256] on credentialsKey [$credentialsKey]: " +
+                "reference count is 0."
+        )
+        return false
     }
 
     override fun count(sha256: String, credentialsKey: String?): Long {