A power supply control system for a vehicle that is provided with a lead-acid battery with comparatively high output density and low energy density, and a lithium-ion battery with comparatively low output density and high energy density. On an engine start that accompanies an ignition operation of a vehicle operator, power is supplied to a starter from the lead-acid battery and the engine is started. On an engine restart that accompanies an idling stop control, power is supplied to the starter from the lithium-ion battery and the engine is started.