A fuel cell system comprises: a DBFC for generating a power by receiving a fuel; a PEMFC for generating a power by receiving hydrogen, a byproduct generated at an anode of the DBFC after a reaction, as a fuel; a supplementary power partially charged by a power generated at the DBFC and the PEMFC and discharging the charged power; a load sensing unit for sensing a load connected to the DBFC, the PEMFC, and the supplementary power; and a control unit for controlling a power of the DBFC, the PEMFC, and the supplementary power according to a load sensed by the load sensing unit and thereby selectively supplying to the load. According to this, hydrogen generated at the DBFC is recycled, and a load amount is sensed thus to stably correspond to a load variation, thereby maximizing a fuel usage efficiency and stably driving the system.