A marine vessel power supply system supplies power to a plurality of propulsion devices each provided with an engine. The system includes a plurality of switching units arranged to turn on and off power supplies to the propulsion devices individually, an operation judgment unit arranged to judge whether the engine of each propulsion device is in an operating state or in a stopped state, and a power supply control unit arranged to turn off a switching unit of the plurality of switching units, when a switching unit is in the ON state and if the engine of the propulsion device corresponding to the switching unit is in a stopped state for not less than a predetermined time.