This invention provides a peripheral control module, a computer system, and an operation method thereof. The peripheral control module is for a computer system. The computer system includes a power switch capable of outputting a power signal. The peripheral control module includes a control unit and a control circuit. The control unit has a program code for controlling a peripheral module. The control circuit is coupled with the power switch and the control unit for receiving the power signal and outputting a switching signal to the control unit, and the control circuit resets the program code to an initial state before the control unit receives the switching signal. This invention further provides a computer system using the peripheral control module and an operation method thereof.