With the development of full electrification of aircraft, electric drive servo valves are gradually used to realize the adjustment of regional flow, pressure and temperature. The new type of aircraft uses a stepping motor to drive the servo valve, which has low control difficulty and large holding torque, which meets the aircraft's requirements for the reliability, controllability and environment of the servo valve. This paper develops a set of debut hybrid stepper motor driven servo valve control system. The system consists of a flight tube bus, a remote interface unit, a remote actuation unit and a stepping motor-driven servo valve. The stepper motor drive is integrated inside the remote actuation unit. The controlled object is a two-phase hybrid stepping motor driven servo valve. In this paper, the dual H-bridge topology and current closed-loop are used to realize the subdivision control of the two-phase hybrid stepping motor, the protection of the double H bridge is realized through the inverse time protection, and the motor torque margin discrimination is realized through the subdivision control duty cycle. The simulation and test results show that in the process of stepping motor control, it can effectively protect the H bridge from burning due to abnormal load, and at the same time, it can effectively monitor the change of load, expanding the application field of stepping motor electric drive servo valve and improving aircraft performance.