A method for manufacturing an integrated circuit package system includes: forming a stack module including: providing a stack die and encapsulating the stack die with an insulating material having a protruding support and a pad connected to the stack die; mounting the stack module on a package base; connecting the pad to the package base; mounting a top die on the protruding support; connecting the top die to the package base; and encapsulating the top die, the package base, and the stack module with a package encapsulant.