A power supply system for a motherboard includes a voltage regulator circuit includes a system power source, and a voltage output terminal, a sampling circuit having an input, and an output receiving a high level sleep signal from a south bridge of the motherboard, a switching circuit having an input, and an output, a power connector having a control terminal connected to the output of the switching circuit, and a power source being connected to the power connector. When the voltage regulator circuit outputs a voltage greater than a predetermined stable voltage to the sampling circuit, the sampling circuit outputs a low level signal to the switching circuit which in return outputs a high level signal to the control terminal of the power connector to cut off power supply from the power source to the system power source.