Roots-type engine is suitable for small power generation system fuelled by waste heat. The disorderly fluctuations of the waste heat source upstream of the power generation process and changes in external environmental factors cause the working parameters of the device to change, which makes the speed of roots engine unstable, and the output power quality of the system is not good. For this problem, this paper starts from the control structure and control strategy to improve the adjustment speed and anti-interference ability of the control system. In this contribution, the model transformation of the dynamic work unit of waste heat power generation device from engineering to theoretical model is performed, the temperature of working gas and the speed of output shaft of roots engine are determined as control objects, and the internal mode control strategy is introduced to optimize the controller of the system. Simulation results are in good agreement with the measurements, which verify that the optimized control system can effectively improve the following ability and anti-interference of the system, and shorten the response time.