A method for adjusting an output of a fuel cell system is capable of estimating a dry state of a fuel cell vehicle by comparing air flow rates, and adjusting a maximum output applicable to the fuel cell vehicle, thus enabling the fuel cell vehicle to be stably driven. The method for adjusting the output of the fuel cell system includes comparing an air flow rate required for driving and an actually introduced air flow rate to calculate an average air flow rate, and calculating an available output of the vehicle using preset mapping data with respect to the average air flow rate.