diff --git a/CHANGELOG.md b/CHANGELOG.md
index 234f0e6570fbf..9c63823d5d315 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Add support for missing proto fields in GRPC FunctionScore and Highlight ([#20169](https://github.com/opensearch-project/OpenSearch/pull/20169))
 
 ### Fixed
+- Fix bug of warm index: FullFileCachedIndexInput was closed error ([#20055](https://github.com/opensearch-project/OpenSearch/pull/20055))
 - Fix flaky test ClusterMaxMergesAtOnceIT.testClusterLevelDefaultUpdatesMergePolicy ([#18056](https://github.com/opensearch-project/OpenSearch/issues/18056))
 - Fix bug in Assertion framework(Yaml Rest test): numeric comparison fails when comparing Integer vs Long (or Float vs Double) ([#19376](https://github.com/opensearch-project/OpenSearch/pull/19376))
 
diff --git a/server/src/main/java/org/opensearch/index/store/remote/filecache/FileCachedIndexInput.java b/server/src/main/java/org/opensearch/index/store/remote/filecache/FileCachedIndexInput.java
index ab6f5f931da0f..fba8dacc1e99e 100644
--- a/server/src/main/java/org/opensearch/index/store/remote/filecache/FileCachedIndexInput.java
+++ b/server/src/main/java/org/opensearch/index/store/remote/filecache/FileCachedIndexInput.java
@@ -13,6 +13,7 @@
 
 import java.io.IOException;
 import java.nio.file.Path;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 /**
  * Reference Counted IndexInput. The first FileCachedIndexInput for a file/block is called origin.
@@ -41,7 +42,7 @@ public class FileCachedIndexInput extends IndexInput implements RandomAccessInpu
     /** indicates if this IndexInput instance is a clone or not */
     protected final boolean isClone;
 
-    protected volatile boolean closed = false;
+    protected final AtomicBoolean closed = new AtomicBoolean(false);
 
     public FileCachedIndexInput(FileCache cache, Path filePath, IndexInput underlyingIndexInput) {
         this(cache, filePath, underlyingIndexInput, false);
@@ -139,7 +140,7 @@ public IndexInput slice(String sliceDescription, long offset, long length) throw
 
     @Override
     public void close() throws IOException {
-        if (!closed) {
+        if (!closed.get()) {
             // if the underlying lucene index input is a clone,
             // the following line won't close/unmap the file.
             luceneIndexInput.close();
@@ -148,7 +149,7 @@ public void close() throws IOException {
             if (isClone) {
                 cache.decRef(filePath);
             }
-            closed = true;
+            closed.set(true);
         }
     }
 }
diff --git a/server/src/main/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInput.java b/server/src/main/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInput.java
index deb8f437bfd63..78ef14b5a9698 100644
--- a/server/src/main/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInput.java
+++ b/server/src/main/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInput.java
@@ -18,6 +18,7 @@
 import java.io.IOException;
 import java.lang.ref.Cleaner;
 import java.nio.file.Path;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 /**
  * Extension of {@link FileCachedIndexInput} for full files for handling clones and slices
@@ -37,7 +38,7 @@ public FullFileCachedIndexInput(FileCache cache, Path filePath, IndexInput under
 
     public FullFileCachedIndexInput(FileCache cache, Path filePath, IndexInput underlyingIndexInput, boolean isClone) {
         super(cache, filePath, underlyingIndexInput, isClone);
-        indexInputHolder = new IndexInputHolder(underlyingIndexInput, isClone, cache, filePath);
+        indexInputHolder = new IndexInputHolder(closed, underlyingIndexInput, isClone, cache, filePath);
         CLEANER.register(this, indexInputHolder);
     }
 
@@ -83,7 +84,7 @@ public IndexInput slice(String sliceDescription, long offset, long length) throw
      */
     @Override
     public void close() throws IOException {
-        if (!closed) {
+        if (!closed.get()) {
             if (isClone) {
                 cache.decRef(filePath);
             }
@@ -93,17 +94,26 @@ public void close() throws IOException {
                 logger.trace("FullFileCachedIndexInput already closed");
             }
             luceneIndexInput = null;
-            closed = true;
+            closed.set(true);
         }
     }
 
+    /**
+     * Run resource cleaning，To be used only in test
+     */
+    public void indexInputHolderRun() {
+        indexInputHolder.run();
+    }
+
     private static class IndexInputHolder implements Runnable {
+        private final AtomicBoolean closed;
         private final IndexInput indexInput;
         private final FileCache cache;
         private final boolean isClone;
         private final Path path;
 
-        IndexInputHolder(IndexInput indexInput, boolean isClone, FileCache cache, Path path) {
+        IndexInputHolder(AtomicBoolean closed, IndexInput indexInput, boolean isClone, FileCache cache, Path path) {
+            this.closed = closed;
             this.indexInput = indexInput;
             this.isClone = isClone;
             this.cache = cache;
@@ -113,8 +123,11 @@ private static class IndexInputHolder implements Runnable {
         @Override
         public void run() {
             try {
-                indexInput.close();
-                if (isClone) cache.decRef(path);
+                if (!closed.get()) {
+                    indexInput.close();
+                    if (isClone) cache.decRef(path);
+                    closed.set(true);
+                }
             } catch (IOException e) {
                 logger.error("Failed to close IndexInput while clearing phantom reachable object");
             }
diff --git a/server/src/test/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInputTests.java b/server/src/test/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInputTests.java
index bc646cc8d50db..cfeb886a5df8a 100644
--- a/server/src/test/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInputTests.java
+++ b/server/src/test/java/org/opensearch/index/store/remote/filecache/FullFileCachedIndexInputTests.java
@@ -78,6 +78,40 @@ public void testSlice() throws IOException {
         assertFalse(isActiveAndTotalUsageSame());
     }
 
+    public void testClose() throws IOException {
+        setupIndexInputAndAddToFileCache();
+
+        // Since the file is already in cache and has refCount 1, activeUsage and totalUsage will be same
+        assertTrue(isActiveAndTotalUsageSame());
+
+        fileCache.decRef(filePath);
+
+        // 3 Clones
+        FullFileCachedIndexInput indexInputClone1 = fullFileCachedIndexInput.clone();
+        FullFileCachedIndexInput indexInputClone2 = fullFileCachedIndexInput.clone();
+        FullFileCachedIndexInput indexInputClone3 = fullFileCachedIndexInput.clone();
+
+        assertEquals((int) fileCache.getRef(filePath), 3);
+        // Close Clone1, refCount -1
+        indexInputClone1.close();
+        assertEquals((int) fileCache.getRef(filePath), 2);
+        // Mock GC resource cleaning, but the deRef function will not be called again.
+        indexInputClone1.indexInputHolderRun();
+        assertEquals((int) fileCache.getRef(filePath), 2);
+
+        // Mock GC resource cleaning, refCount -1
+        indexInputClone2.indexInputHolderRun();
+        assertEquals((int) fileCache.getRef(filePath), 1);
+        // Close Clone2, but the deRef function will not be called again.
+        indexInputClone2.close();
+        assertEquals((int) fileCache.getRef(filePath), 1);
+
+        indexInputClone3.close();
+        assertEquals((int) fileCache.getRef(filePath), 0);
+        indexInputClone3.indexInputHolderRun();
+        assertEquals((int) fileCache.getRef(filePath), 0);
+    }
+
     private void triggerGarbageCollectionAndAssertClonesClosed() {
         try {
             // Clones/Slices will be phantom reachable now, triggering gc should call close on them