A control system and method for preventing a fuel cell from overheating are disclosed. The system includes: a fuel cell that generates electric power through reaction of fuel gas and oxidation gas; a cooling line in which a cooling medium flows and performs heat exchange with the fuel cell; a cooling pump installed on the cooling line and configured to circulate the cooling medium through the cooling line; a cooling controller that controls an operating state of the cooling pump on the basis of the temperature of the fuel cell or the cooling medium; and a power generation controller that limits power generation of the fuel cell on the basis of the operating state of the cooling pump.