A power supply apparatus with a protection function includes a pulse width modulation control unit, a pulse width modulation detecting unit, a switch unit and a feedback circuit. The feedback circuit detects a bus voltage. When the feedback circuit detects that the bus voltage is greater than a predetermined voltage, the feedback circuit sends an informing signal to the pulse width modulation control unit. The pulse width modulation control unit adjusts a duty cycle of a pulse width modulation signal and sends the pulse width modulation signal to the pulse width modulation detecting unit. When the pulse width modulation detecting unit detects that the duty cycle of the pulse width modulation signal is less than a predetermined cycle, the pulse width modulation detecting unit turns off the switch unit to stop outputting power to avoid a reverse current phenomenon.