A power supply system that includes two secondary batteries having different charge and discharge characteristics and is mountable on a vehicle. The power supply system has a lead-acid storage battery connected to an electrical load; a lithium-ion storage battery connected in parallel with the lead-acid storage battery with respect to the electrical load; a power generator configured to charge the lead-acid storage battery and the lithium-ion storage battery; and a control unit configured to drive the power generator based on a relationship between a discharge current of the lead-acid storage battery and a discharge current of the lithium-ion storage battery.