A power supply system mounted in a vehicle. A rotary machine is connected to an output shaft of an internal-combustion engine of the vehicle, and has a power generation function, an engine start-up function, and an engine output assist function. A first secondary battery and a second secondary battery are each electrically connected in parallel with the rotary machine. A connection switch is provided along a connecting line electrically connecting the first and second secondary batteries, where the connection switch is configured to electrically connect and disconnect the second secondary battery and a parallel connection of the first secondary battery and the rotary machine. A switch controller is configured to disconnect the second secondary battery and the parallel connection by controlling the connection switch to a current cut-off state during the engine start-up and during engine output assist.