In this paper, a variable structure controller for temperature control of the solid oxide fuel cell (SOFC) is proposed. The performance and availability of the SOFC are greatly dependent on its operating temperature. For high efficiency and low degradation of the fuel cell due to thermal cycling, the fuel cell temperature should remain fairly constant during operation. To meet the demands of developing valid control strategies, a control-oriented multi-input multi-output nonlinear thermal model of the SOFC is first developed in this paper. Then, by combining the technique of input-output linearization with variable structure control (VSC) theory, a VSC controller for temperature control is proposed. Simulation results demonstrate the correctness of the proposed control-oriented nonlinear thermal model, while the excellence of the VSC controller for temperature control in the presence of external disturbance is proved.