The object of this invention is to provide a fuel supply system capable of reducing the quantity of a fuel to be discharged from a plurality of fuel tanks connected in parallel is provided. The fuel supply system includes a plurality of the fuel tanks for storing a fuel, on-off valves provided individually for the fuel tanks, and a control unit which controls the opening and closing of the on-off valves. The control unit changes the number of the on-off valves to be simultaneously opened according to a situation. The control unit may reduce the number of the on-off valves to be simultaneously opened after a failure is detected or at the time of maintenance of the fuel supply system.