Thermoelectric power generation using the thermoelectric power generation element is now being developed as one of the future power generation systems by thermal energy. However, the system has some problems of improving the generating efficiency. In this paper, an operator-based nonlinear control system for the thermoelectric power generation system is proposed. Firstly, structure of the thermoelectric power generation system is introduced. Secondly, the thermoelectric power generation system is modeled and the proposed system based an operator-theory is designed by using the model. Finally, the effectiveness of the proposed control system is confirmed by simulation results and experimental results.