The invention provides a power supply system used in a computer and a power supply method thereof; wherein, the power supply method, which is applied to a first power supply and a second power supply and provides a first voltage for a mainboard, includes the following steps: whether the first voltage of the first power supply and the first voltage of the second power supply reach steady state is detected; when the first voltage of the first power supply reaches steady state, the first voltage of the first power supply is connected to a first pin; when the first voltage of the second power supply reaches steady state, the first voltage of the second power supply is connected to the first pin; moreover, the pin is used for providing the first voltage for the mainboard. With a power supply keyset which has sequential control function and is arranged in the parallel connection double-set power supply system of the invention, as long as one of the two sets of power supplies can be normallystarted and establishes the voltage required by the mainboard, the power supply can provide electricity for the mainbody.