The present invention discloses a fuel cell system, which comprises a fuel cell stack, a gas delivery system, and a control system, wherein the fuel cell stack is coupled to a load and is used to provide power, and the gas delivery system is coupled to the fuel cell stack and is used to provide the fuel cell stack with fuel and oxygen. The control system comprises a feedforward controller and a correction controller, wherein the feedforward controller is used to generate an expected control instruction signal based on a command from the load, and the correction controller is used to generate a control correction signal based on at least one measurement signal from the fuel cell system to prevent from violating an operation constraint of the fuel cell stack. The control system generates a control signal based on the expected control instruction signal and the control correction signal, and controls the gas delivery system based on the generated control signal, so as to ensure that the fuel cell stack runs in a safe operation limit. The present invention further discloses a method for controlling the fuel cell system.