A fuel cell system of this disclosure includes a fuel cell stack; a water supply unit to selectively supply cooling water or heated water to a cooler of the fuel cell stack, and including a heater for heating the cooling water; an air cutoff valve to supply air to an anode of the fuel cell stack and drain a residue from the anode; an anode pressure regulator to drain the residue from the air cutoff valve and control a pressure of the anode; sensors to measure an operating temperature of the fuel cell stack, an outside air temperature, and an atmospheric pressure; and a controller to calculate a target pressure for the anode, control the air cut-off valve, control the anode pressure regulator, and stop an operation of the heater when a stack voltage of the fuel cell stack is lower than a predetermined reference voltage.