Nowadays, the temperature gradient is considered as one of the most important parameters which impact the performance of the solid oxide fuel cell (SOFC). In this paper, a control strategy based on an input–output feedback linearization technology is derived for controlling the maximum temperature gradient within the anode fuel flow channel at the desired value. For the controller design, the temperature dynamic model is proposed and simplified to a control-oriented multi-input and multioutput nonlinear dynamic model. Then, this paper presents an input–output feedback linearization controller to realize the control objective by adjusting the cathode input air flow. Finally, the simulation results are given to demonstrate the accuracy of the proposed model in reflecting the temperature dynamic characteristics. Moreover, the compound controller is added for simulation as a comparison, which shows that the proposed controller is equipped with better effectiveness and efficiency in the presence of external disturbances.