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A new solid oxide fuel cell (SOFC) system structure is proposed in this paper. Two bypass valves, a desiccator and a blower are added in our previous system. The temperatures of system components could be controlled more easily and successfully, because two degree of freedom is increased by the two added bypass valves. The two different system structures are compared in figure 1. Then, a controller is designed to make sure that all the system components are working within safe temperature ranges when the SOFC system is in stability and on a power switching transient. The controller is operated with a three-level target: a) temperature security, b) load following, c) system efficiency. This target means that the SOFC system must be operating in a safety temperature range all the time. Then load following needs to be accomplished in a short time. Finally, the system efficiency will be considered. The simulation results show that this new system structure could increase the system efficiency and make the temperatures of system components easier to be controlled. The simulation results also prove that the designed controller is effective.