With the development of multi-/all-electric technology, more and more aircraft platforms use electrically driven servo valves as the driving source to realize real-time adjustments of flow, pressure and temperature in the area network. The new generation of aircraft applies a stepper motor to drive the servo valve as the drive source, and utilizes the holding torque and open-loop control characteristics of the stepper motor when the stepper motor could not meet aircraft’s requirements of the reliability of the servo valve, the controllability of the opening and closing angle, and the environmental resistance. This paper develops a set of stepper motor drive servo valve control system. The system is mainly composed of flight tube bus, electromechanical management computer, remote actuation unit, remote interface unit and motor-driven servo valve. The stepper motor driver is integrated in the remote execution unit and is used to control the two-phase hybrid stepper motor to drive the servo valve. The topology of a three-phase inverter bridge drive is used to achieve the two-phase double four-shot drive, which saves about 25% power drive hardware. By controlling the two-phases motor, the direction and amplitude of the current one can realize micro-step control. The test and simulation result show that the system has higher control accuracy and better acceleration. The deceleration characteristics in two-phase full step and micro step working modes can expand the application of electric servo valve and improve aircraft performance.