A method for controlling a fuel cell system, the method comprising: calculating, by a processor, a fuel cell demand current based on a driver demand current calculated from a driver demand torque; calculating, by the processor, a first target flow rate of air to be supplied to a fuel cell stack based on the fuel cell demand current and a target stoichiometric ratio, SR, of air, wherein the target SR is calculated according to a relative humidity value of the fuel cell stack; calculating, by the processor, a calculated SR based on an air flow rate and a fuel cell current, wherein the calculated SR is equal to the air flow rate divided by the fuel cell current multiplied by a constant; compensating, by the processor, for the first target flow rate using the target SR and the calculated SR, including the steps: calculating an SR ratio of the calculated SR of air to the target SR; determining whether the calculated SR ratio is a value between a predetermined minimum value and a predetermined maximum value; and setting the first target flow rate to a second target flow rate without compensation if the SR ratio is not a value between the minimum value and the maximum value, and calculating the second target flow rate by compensating the first target flow rate by the following equation, E1, if the SR ratio is a value between the minimum value and the maximum value: second target flow rate = first target flow rate / SR Ratio × Compensation coefficient; calculating, by the processor, a revolutions per minute, RPM, command value of an air blower based on the compensated second target flow rate and the amount of air currently measured; and controlling the operation of the air blower based on the calculated RPM command value. calculating, by a processor, a fuel cell demand current based on a driver demand current calculated from a driver demand torque; calculating, by the processor, a first target flow rate of air to be supplied to a fuel cell stack based on the fuel cell demand current and a target stoichiometric ratio, SR, of air, wherein the target SR is calculated according to a relative humidity value of the fuel cell stack; calculating, by the processor, a calculated SR based on an air flow rate and a fuel cell current, wherein the calculated SR is equal to the air flow rate divided by the fuel cell current multiplied by a constant; compensating, by the processor, for the first target flow rate using the target SR and the calculated SR, including the steps: calculating an SR ratio of the calculated SR of air to the target SR; determining whether the calculated SR ratio is a value between a predetermined minimum value and a predetermined maximum value; and setting the first target flow rate to a second target flow rate without compensation if the SR ratio is not a value between the minimum value and the maximum value, and calculating the second target flow rate by compensating the first target flow rate by the following equation, E1, if the SR ratio is a value between the minimum value and the maximum value: second target flow rate = first target flow rate / SR Ratio × Compensation coefficient; calculating, by the processor, a revolutions per minute, RPM, command value of an air blower based on the compensated second target flow rate and the amount of air currently measured; and controlling the operation of the air blower based on the calculated RPM command value.