Abstract: A power supply system and operating method thereof are provided. The power supply system includes a power generation circuit and a discharge circuit. The power generation circuit is configured to provide an output voltage at an output end when a power is started, and stop providing the output voltage when the power is off. The discharge circuit includes a capacitor, a comparison circuit, and a switch circuit. The comparison circuit is configured to compare a voltage at a detection end and the output voltage at the output end to generate a comparison result. The switch circuit is configured to discharge the output end according to the comparison result when the power is off. The power supply system and an operating method thereof provided by the disclosure can reduce loss when the power is off, so as to improve the operation quality of the circuit.