The rotary electric actuator system adopts NGWN planetary gears as the main transmission mode, and when it operates under conditions requiring frequent direction changes, the gear gap can cause torque fluctuations and destructive switching impacts. In order to meet the strict demands of the electric actuator system for enhanced stability, reliability and fast response capability, the actuator gap and stiffness are identified by the recursive least-squares method containing elements of the genetic algorithm, and an electromechanical coupling model is established based on the identification results, and a comprehensive optimal control method combining adaptive acceleration backlash compensation and sliding-mode control is proposed, and the optimal control algorithm is verified through simulation and combined with the experimental data. The optimized control algorithm is verified by simulation and experimental data to have good suppression effect on the actuator commutation shock.