A computer system and its booting and setting method are disclosed. Power supplying and a booting process of the computer system are controlled by a basic input/output system (BIOS). The computer system includes a super input/output chip, a south bridge chipset, and a power supply module. The super input/output chip includes a timer. A counting time is set by the BIOS and the timer counts down when booting the computer system, wherein the counting time is longer than a normal booting time. The south bridge chipset is electrically connected with the super input/output chip and exchanges data between a south bridge chipset and a peripheral device. The power supply module is used for providing power to the computer system. The BIOS controls the timer to stop counting down when the computer system is capable of booting normally.