A power supply system capable of obtaining a high output with a good startability even in an extremely low humidity atmosphere. The power supply system includes a hybrid structure of a humidified type fuel cell unit using as an electrolyte a humidified type proton conductor having a proton conductive function in a humidified state and a low-grade humidified type fuel cell unit using as an electrolyte a low-grade humidified type proton conductor developing a proton conductive function in a humidified state lower than the above-mentioned humidified state. At the time of initial start-up, at least the low-grade humidified type fuel cell unit is operated, and then only the humidified type fuel cell unit is operated. At the time of initial start-up, moisture generated in the low-grade humidified type fuel cell unit is supplied to the electrolyte of the humidified type fuel cell unit.