diff --git a/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/rewrite/PruneEmptyPartition.java b/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/rewrite/PruneEmptyPartition.java
index c7b8f452afbe66..3347518b1652a8 100644
--- a/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/rewrite/PruneEmptyPartition.java
+++ b/fe/fe-core/src/main/java/org/apache/doris/nereids/rules/rewrite/PruneEmptyPartition.java
@@ -18,11 +18,16 @@
 package org.apache.doris.nereids.rules.rewrite;
 
 import org.apache.doris.catalog.OlapTable;
+import org.apache.doris.catalog.Partition;
 import org.apache.doris.nereids.rules.Rule;
 import org.apache.doris.nereids.rules.RuleType;
 import org.apache.doris.nereids.trees.plans.logical.LogicalEmptyRelation;
 import org.apache.doris.nereids.trees.plans.logical.LogicalOlapScan;
 import org.apache.doris.qe.ConnectContext;
+import org.apache.doris.transaction.TransactionEntry;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 
 import java.util.List;
 
@@ -30,6 +35,7 @@
  * Used to prune empty partition.
  */
 public class PruneEmptyPartition extends OneRewriteRuleFactory {
+    public static final Logger LOG = LogManager.getLogger(PruneEmptyPartition.class);
 
     @Override
     public Rule build() {
@@ -38,6 +44,11 @@ public Rule build() {
             OlapTable table = scan.getTable();
             List<Long> partitionIdsToPrune = scan.getSelectedPartitionIds();
             List<Long> ids = table.selectNonEmptyPartitionIds(partitionIdsToPrune);
+            if (ctx.connectContext != null && ctx.connectContext.isTxnModel()) {
+                // In transaction load, need to add empty partitions which have invisible data of sub transactions
+                selectNonEmptyPartitionIdsForTxnLoad(ctx.connectContext.getTxnEntry(), table, scan.getSelectedIndexId(),
+                        partitionIdsToPrune, ids);
+            }
             if (ids.isEmpty()) {
                 return new LogicalEmptyRelation(ConnectContext.get().getStatementContext().getNextRelationId(),
                         scan.getOutput());
@@ -49,4 +60,24 @@ public Rule build() {
             return scan.withSelectedPartitionIds(ids);
         }).toRule(RuleType.PRUNE_EMPTY_PARTITION);
     }
+
+    private void selectNonEmptyPartitionIdsForTxnLoad(TransactionEntry txnEntry, OlapTable table, long indexId,
+            List<Long> selectedPartitions, List<Long> nonEmptyPartitionIds) {
+        for (Long selectedPartitionId : selectedPartitions) {
+            if (nonEmptyPartitionIds.contains(selectedPartitionId)) {
+                continue;
+            }
+            Partition partition = table.getPartition(selectedPartitionId);
+            if (partition == null) {
+                continue;
+            }
+            if (!txnEntry.getPartitionSubTxnIds(table.getId(), partition, indexId).isEmpty()) {
+                nonEmptyPartitionIds.add(selectedPartitionId);
+            }
+        }
+        if (LOG.isDebugEnabled()) {
+            LOG.debug("add partition for txn load, table: {}, selected partitions: {}, non empty partitions: {}",
+                    table.getId(), selectedPartitions, nonEmptyPartitionIds);
+        }
+    }
 }
diff --git a/fe/fe-core/src/main/java/org/apache/doris/transaction/TransactionEntry.java b/fe/fe-core/src/main/java/org/apache/doris/transaction/TransactionEntry.java
index 25c4ff4b3b2493..70c281201b6f66 100644
--- a/fe/fe-core/src/main/java/org/apache/doris/transaction/TransactionEntry.java
+++ b/fe/fe-core/src/main/java/org/apache/doris/transaction/TransactionEntry.java
@@ -22,7 +22,9 @@
 import org.apache.doris.catalog.DatabaseIf;
 import org.apache.doris.catalog.Env;
 import org.apache.doris.catalog.KeysType;
+import org.apache.doris.catalog.MaterializedIndex;
 import org.apache.doris.catalog.OlapTable;
+import org.apache.doris.catalog.Partition;
 import org.apache.doris.catalog.Table;
 import org.apache.doris.catalog.TableIf;
 import org.apache.doris.cloud.transaction.CloudGlobalTransactionMgr;
@@ -501,6 +503,30 @@ public void setTxnLoadInfoInObserver(TTxnLoadInfo txnLoadInfo) throws DdlExcepti
                 + "subTxnStates={}", label, transactionId, dbId, timeoutTimestamp, allSubTxnNum, subTransactionStates);
     }
 
+    public List<Long> getPartitionSubTxnIds(long tableId, Partition partition, long indexId) {
+        List<Long> subTxnIds = new ArrayList<>();
+        MaterializedIndex index = partition.getIndex(indexId);
+        if (index == null) {
+            LOG.error("index={} not found in table={}, partition={}", indexId, tableId, partition.getId());
+            return subTxnIds;
+        }
+        for (SubTransactionState subTransactionState : subTransactionStates) {
+            if (subTransactionState.getTable().getId() != tableId) {
+                continue;
+            }
+            for (TTabletCommitInfo tabletCommitInfo : subTransactionState.getTabletCommitInfos()) {
+                if (index.getTablet(tabletCommitInfo.getTabletId()) != null) {
+                    subTxnIds.add(subTransactionState.getSubTransactionId());
+                    break;
+                }
+            }
+        }
+        if (LOG.isDebugEnabled()) {
+            LOG.debug("table_id={}, partition_id={}, sub_txn_ids={}", tableId, partition.getId(), subTxnIds);
+        }
+        return subTxnIds;
+    }
+
     private void resetByTxnInfo(TTxnLoadInfo txnLoadInfo) throws DdlException {
         if (txnLoadInfo.isSetDbId()) {
             this.dbId = txnLoadInfo.getDbId();
diff --git a/regression-test/suites/insert_p0/transaction/txn_insert.groovy b/regression-test/suites/insert_p0/transaction/txn_insert.groovy
index 41b8a6d35dd909..319a20fdaba27d 100644
--- a/regression-test/suites/insert_p0/transaction/txn_insert.groovy
+++ b/regression-test/suites/insert_p0/transaction/txn_insert.groovy
@@ -793,6 +793,28 @@ suite("txn_insert") {
             order_qt_select_cu2 """select * from ${unique_table}_2"""
             order_qt_select_cu3 """select * from ${unique_table}_3"""
         }
+
+        // 19. delete from empty table
+        sql """ drop table if exists txn_insert_dt6; """
+        sql """
+            CREATE TABLE `txn_insert_dt6` (
+                `ID` int NOT NULL,
+                `NAME` varchar(100) NULL,
+                `SCORE` int NULL
+            ) ENGINE=OLAP
+            DUPLICATE KEY(`ID`)
+            DISTRIBUTED BY HASH(`ID`) BUCKETS 1
+            PROPERTIES (
+                "replication_allocation" = "tag.location.default: 1"
+            ); 
+        """
+        sql """ begin; """
+        sql """ INSERT INTO txn_insert_dt6 select 1, 'Alice', 100; """
+        test {
+            sql """ delete from txn_insert_dt6 where id = 1; """
+            exception """Can not delete because there is a insert operation for the same table"""
+        }
+        sql """ rollback; """
     }
 
     def db_name = "regression_test_insert_p0_transaction"