diff --git a/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/DeletionData.java b/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/DeletionData.java
index 186426650fe50..dc4908ef2c38f 100644
--- a/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/DeletionData.java
+++ b/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/DeletionData.java
@@ -59,6 +59,10 @@ public void serialize(DataOutputStream stream) throws IOException {
     deletion.serializeWithoutFileOffset(stream);
   }
 
+  public Deletion getModEntry() {
+    return this.deletion;
+  }
+
   public static DeletionData deserialize(InputStream stream)
       throws IllegalPathException, IOException {
     return new DeletionData(Deletion.deserializeWithoutFileOffset(new DataInputStream(stream)));
diff --git a/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/TsFileSplitter.java b/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/TsFileSplitter.java
index af401f84aa777..4571bdb1531d2 100644
--- a/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/TsFileSplitter.java
+++ b/iotdb-core/datanode/src/main/java/org/apache/iotdb/db/storageengine/load/splitter/TsFileSplitter.java
@@ -156,7 +156,6 @@ private void processTimeChunkOrNonAlignedChunk(TsFileSequenceReader reader, byte
     long chunkOffset = reader.position();
     timeChunkIndexOfCurrentValueColumn = pageIndex2TimesList.size();
     consumeAllAlignedChunkData(chunkOffset, pageIndex2ChunkData);
-    handleModification(offset2Deletions, chunkOffset);
 
     ChunkHeader header = reader.readChunkHeader(marker);
     String measurementId = header.getMeasurementID();
diff --git a/iotdb-core/datanode/src/test/java/org/apache/iotdb/db/storageengine/dataregion/compaction/BatchedCompactionWithTsFileSplitterTest.java b/iotdb-core/datanode/src/test/java/org/apache/iotdb/db/storageengine/dataregion/compaction/BatchedCompactionWithTsFileSplitterTest.java
index 37d38411ff671..1a407648a51f2 100644
--- a/iotdb-core/datanode/src/test/java/org/apache/iotdb/db/storageengine/dataregion/compaction/BatchedCompactionWithTsFileSplitterTest.java
+++ b/iotdb-core/datanode/src/test/java/org/apache/iotdb/db/storageengine/dataregion/compaction/BatchedCompactionWithTsFileSplitterTest.java
@@ -22,6 +22,7 @@
 import org.apache.iotdb.common.rpc.thrift.TTimePartitionSlot;
 import org.apache.iotdb.commons.exception.IllegalPathException;
 import org.apache.iotdb.commons.exception.MetadataException;
+import org.apache.iotdb.commons.path.MeasurementPath;
 import org.apache.iotdb.db.conf.IoTDBDescriptor;
 import org.apache.iotdb.db.exception.StorageEngineException;
 import org.apache.iotdb.db.exception.load.LoadFileException;
@@ -30,10 +31,15 @@
 import org.apache.iotdb.db.storageengine.dataregion.compaction.execute.task.CompactionTaskSummary;
 import org.apache.iotdb.db.storageengine.dataregion.compaction.execute.utils.CompactionUtils;
 import org.apache.iotdb.db.storageengine.dataregion.compaction.utils.CompactionCheckerUtils;
+import org.apache.iotdb.db.storageengine.dataregion.compaction.utils.CompactionTestFileWriter;
+import org.apache.iotdb.db.storageengine.dataregion.modification.Deletion;
+import org.apache.iotdb.db.storageengine.dataregion.modification.Modification;
+import org.apache.iotdb.db.storageengine.dataregion.modification.ModificationFile;
 import org.apache.iotdb.db.storageengine.dataregion.tsfile.TsFileResource;
 import org.apache.iotdb.db.storageengine.dataregion.tsfile.generator.TsFileNameGenerator;
 import org.apache.iotdb.db.storageengine.dataregion.utils.TsFileResourceUtils;
 import org.apache.iotdb.db.storageengine.load.splitter.AlignedChunkData;
+import org.apache.iotdb.db.storageengine.load.splitter.DeletionData;
 import org.apache.iotdb.db.storageengine.load.splitter.TsFileData;
 import org.apache.iotdb.db.storageengine.load.splitter.TsFileSplitter;
 
@@ -54,7 +60,9 @@
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.DataOutputStream;
+import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -233,6 +241,84 @@ public void testCompactionFlushPageAndSplitByTimePartition()
     consumeChunkDataAndValidate(targetResource);
   }
 
+  @Test
+  public void testDeletionDataShouldOnlyBeGeneratedOnceAtEnd()
+      throws IOException, MetadataException, LoadFileException, IllegalPathException {
+    TsFileResource resource = createAlignedMultiDeviceFile();
+    try (ModificationFile modificationFile = ModificationFile.getNormalMods(resource)) {
+      modificationFile.write(
+          new Deletion(new MeasurementPath("root.testsg.d0.s0"), Long.MAX_VALUE, 100));
+      modificationFile.write(
+          new Deletion(new MeasurementPath("root.testsg.d0.s1"), Long.MAX_VALUE, 200));
+      modificationFile.write(
+          new Deletion(new MeasurementPath("root.testsg.d1.s0"), Long.MAX_VALUE, 300));
+      modificationFile.write(
+          new Deletion(new MeasurementPath("root.testsg.d1.s1"), Long.MAX_VALUE, 400));
+    }
+
+    List<Modification> expectedMods =
+        new ArrayList<>(ModificationFile.getNormalMods(resource).getModifications());
+    List<Modification> deletionMods = new ArrayList<>();
+    File actualModsFile = new File(resource.getTsFilePath() + ".mods");
+    try (ModificationFile actualModificationFile =
+        new ModificationFile(actualModsFile.getAbsolutePath())) {
+      TsFileSplitter splitter =
+          new TsFileSplitter(
+              resource.getTsFile(),
+              tsFileData -> {
+                if (tsFileData instanceof DeletionData) {
+                  deletionMods.add(((DeletionData) tsFileData).getModEntry());
+                }
+                return true;
+              });
+      splitter.splitTsFileByDataPartition();
+    }
+
+    List<Modification> actualMods;
+    try (ModificationFile actualModificationFile =
+        new ModificationFile(actualModsFile.getAbsolutePath())) {
+      actualMods = new ArrayList<>(actualModificationFile.getModifications());
+    }
+    Assert.assertEquals(expectedMods, actualMods);
+    Files.deleteIfExists(actualModsFile.toPath());
+  }
+
+  private TsFileResource createAlignedMultiDeviceFile() throws IOException {
+    TsFileResource resource = createEmptyFileAndResource(true);
+    try (CompactionTestFileWriter writer = new CompactionTestFileWriter(resource)) {
+      writer.startChunkGroup("d0");
+      writer.generateSimpleAlignedSeriesToCurrentDeviceWithNullValue(
+          Arrays.asList("s0", "s1"),
+          new TimeRange[][] {
+            new TimeRange[] {new TimeRange(1, 100), new TimeRange(200, 300)},
+            new TimeRange[] {
+              new TimeRange(604799900, 604800020), new TimeRange(604810020, 604820020)
+            }
+          },
+          TSEncoding.PLAIN,
+          CompressionType.LZ4,
+          Arrays.asList(false, false));
+      writer.endChunkGroup();
+
+      writer.startChunkGroup("d1");
+      writer.generateSimpleAlignedSeriesToCurrentDeviceWithNullValue(
+          Arrays.asList("s0", "s1"),
+          new TimeRange[][] {
+            new TimeRange[] {new TimeRange(1, 100), new TimeRange(200, 300)},
+            new TimeRange[] {
+              new TimeRange(604799900, 604800020), new TimeRange(604810020, 604820020)
+            }
+          },
+          TSEncoding.PLAIN,
+          CompressionType.LZ4,
+          Arrays.asList(false, false));
+      writer.endChunkGroup();
+
+      writer.endFile();
+    }
+    return resource;
+  }
+
   private TsFileResource performCompaction()
       throws StorageEngineException,
           IOException,