In the new green Eco-toilet, the temperature of the reaction chamber plays a crucial role in the effective decomposition and utilization of human excreta. In this paper, an FPGA-based reaction chamber thermal control system is proposed. The system combines with explosion-proof temperature sensor and DC water pump, which can control and keep the temperature of reaction chamber in a proper range. The experimental results show the efficacy of the system, demonstrating that the proposed system can promote the development of new green Eco-toilet.