A power supplying control method of a computer system for use with a first power supply and a second power supply both providing a first specific voltage to a motherboard, including steps of: detecting whether the first power supply and the second power supply, outputting the first specific voltage, are at a stable state; outputting the first specific voltage to a first pin when the first power supply is at the stable state; outputting the first specific voltage to the first pin when the second power supply is at the stable state; and outputting the first specific voltage to the motherboard via the first pin.