A power supply system for a motherboard includes a switching power source, a control circuit, and a switch circuit. The control circuit includes a photocoupler and a comparator. The photocoupler is electrically connected to the switching power source and the comparator. The switch circuit is electrically connected to the comparator and a motherboard. The switch circuit is turned off when the motherboard is in a normal state and turned on when the motherboard is in a standby state. The switching power source outputs a voltage through the control circuit when the switch circuit is turned off. When the switch circuit is turned on, the comparator outputs a first state signal to the photocoupler. The photocoupler thus outputs a first driving signal to the switching power source. The first driving signal causes the switching power source to reduce the voltage.