A fuel cell system and a control method thereof are capable of preventing anode flooding due to a temperature difference between a stack and reformate upon starting a fuel cell system. The method of controlling a fuel cell system including steps of detecting a temperature of a fuel cell stack, detecting a temperature of reformate that is generated in a fuel reformer and then is supplied to the fuel cell stack through a heat exchanger, and setting the temperature of the reformate to be lower than the temperature of the fuel cell stack during a starting time of the fuel cell system.