Temperature control system and method for a fuel cell system are disclosed. The temperature control system includes a state detector, a control selector, a normal controller and an internal model controller. The state detector determines whether the fuel cell system is in a leakage condition based on a dynamic transfer function from an air flowrate provided to the fuel cell system to a fuel cell temperature. The control selector selects to switch between the normal controller and the internal model controller based on a determined result. The normal controller is configured for controlling an air flowrate of the fuel cell system which is not in the leakage condition. The internal model controller is configured for controlling the air flowrate of the fuel cell system in the leakage condition to control the fuel cell temperature. A fuel cell system with the temperature control system is also disclosed.