A control circuit and control method of electric output modes for a stacked power supply system which has a circuit board to integrate a plurality of power supply devices to output electricity. The circuit board has a control circuit to actuate the power supply devices. The control circuit provides a parallel power supply mode and a backup power supply mode, and is connected to a switch device which provides a first signal source and a second signal source corresponding to the parallel power supply mode and the backup power supply mode to enable users to select an actuation signal output from the control circuit to determine the parallel power supply mode or backup power supply mode of the power supply devices.