how to overwrite system default keyboard shortcuts like Ctrl+C, Ctrl+V by using Javafx KeyCombination?

The problem is the behavior of TextArea (which is an internal class) adds a number of EventHandlers which handle various user-generated events (e.g. key presses). This includes the common shortcuts used for cut, copy, paste, undo, redo, select all, and so on. These handlers then consume the event which stops said event's propagation. Since menu item accelerators only work when the event bubbles back up to the Scene, the event being consumed by the TextArea behavior means your menu items don't fire.

One workaround is to use a custom EventDispatcher on the TextArea to filter out any key events which match any of a number of key combinations. All other events are allowed to proceed normally, leaving the rest of the behavior intact. This works by preventing the event from reaching the TextArea and letting the event enter the bubbling phase of event propagation, ultimately letting the event bubble back up the scene graph. That last bit is why using an EventDispatcher is necessary instead of an event filter; consuming an event in an event filter will stop the event from reaching the TextArea but won't let it bubble back up the scene graph.

Here's an example:

import java.util.Set;
import javafx.application.Application;
import javafx.event.Event;
import javafx.event.EventDispatchChain;
import javafx.event.EventDispatcher;
import javafx.scene.Scene;
import javafx.scene.control.Menu;
import javafx.scene.control.MenuBar;
import javafx.scene.control.MenuItem;
import javafx.scene.control.TextArea;
import javafx.scene.input.KeyCombination;
import javafx.scene.input.KeyEvent;
import javafx.scene.layout.Priority;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class Main extends Application {

  @Override
  public void start(Stage primaryStage) {
    MenuItem cutItem = new MenuItem("Cut");
    cutItem.setAccelerator(KeyCombination.valueOf("shortcut+x"));
    cutItem.setOnAction(e -> System.out.println("CUT"));

    MenuItem copyItem = new MenuItem("Copy");
    copyItem.setAccelerator(KeyCombination.valueOf("shortcut+c"));
    copyItem.setOnAction(e -> System.out.println("COPY"));

    MenuItem pasteItem = new MenuItem("Paste");
    pasteItem.setAccelerator(KeyCombination.valueOf("shortcut+v"));
    pasteItem.setOnAction(e -> System.out.println("PASTE"));

    TextArea area = new TextArea();
    area.setEventDispatcher(
        new FilteringEventDispatcher(
            area.getEventDispatcher(),
            cutItem.getAccelerator(),
            copyItem.getAccelerator(),
            pasteItem.getAccelerator()));

    VBox root = new VBox(new MenuBar(new Menu("Edit", null, cutItem, copyItem, pasteItem)), area);
    VBox.setVgrow(area, Priority.ALWAYS);

    primaryStage.setScene(new Scene(root, 600, 400));
    primaryStage.show();
  }

  private static class FilteringEventDispatcher implements EventDispatcher {

    private final EventDispatcher delegate;
    private final Set<KeyCombination> blacklistedCombos;

    public FilteringEventDispatcher(EventDispatcher delegate, KeyCombination... blacklistedCombos) {
      this.delegate = delegate;
      // Set.of was added in Java 9
      this.blacklistedCombos = Set.of(blacklistedCombos);
    }

    @Override
    public Event dispatchEvent(Event event, EventDispatchChain tail) {
      if (!(event instanceof KeyEvent) || isPermitted((KeyEvent) event)) {
        return delegate.dispatchEvent(event, tail); // forward event to TextArea
      }
      return event; // skip TextArea and enter the bubbling phase
    }

    private boolean isPermitted(KeyEvent event) {
      return blacklistedCombos.stream().noneMatch(combo -> combo.match(event));
    }
  }
}

If necessary, you can filter more specifically by testing the EventType of the event (e.g. only filter KEY_PRESSED events). You could also whitelist combos instead of blacklisting them, depending on your needs.

As I couldn't find proper solution, I have tried some work around for now by adding onKeyPress event handler and it's executing the handler implementation even for Ctrl+C,Ctrl+V etc.

        MenuItem paste = new MenuItem("Paste");
        this.textArea.addEventHandler(KeyEvent.KEY_PRESSED,event -> {
            if(event.isControlDown()&& event.getCode()==KeyCode.V){
                System.out.println("Ctrl+V is triggered");
                if(clipboard.hasString()){
                    String pastedText = clipboard.getString();
                    InsertCommand insertCommand = new InsertCommand(textArea.getCaretPosition(),pastedText,textArea);
                    insertCommand.execute();
                    UndoRedo.insertIntoUndoStack(insertCommand);
                }
            }
        });

Note: still not clear about why it's not working with KeyCombination. if anyone has answer please post it.