I want to control my program with only System Tray Icon so is there any way to remove the Taskbar Icon ?

This is not possible with GLFW (the window implementation used by LWJGL 3). But you can do it with SWT: http://www.java2s.com/Tutorial/Java/0280__SWT/Placeaniconwithapopupmenuonthesystemtray.htm

And then when the user clicks on the tray icon (or on a context menu item), you could show your GLFW window. That means, you _can_ hide a GLFW window for it to not be displayed and also not occupy a slot in the task bar.