A control scheme for the electromechanical actuator systems in air-to-air missiles was propose based on main modal of a transmission mechanism. and a double-loop control system was designed by matching mechanism dynamic characteristics and main modal method. Firstly, a connecting rod from crank slider mechanism was analyzed and the high order multi-degree-of-freedom dynamic model was simplified into two-degree-of-freedom free rotor model by matching mechanism dynamic characteristics and the main modal method. Then, the two-degree-of-freedom model and control system were modeled jointly to analyze the influence of main resonator model on the cutoff frequency of open-loop system with or without damping states. By which it makes sure that it is more reliable when the system is analyzed at the undamped state. Finally, a modal test was performed for the transmission mechanism and the feasibility of modal dynamic characteristic matching method was confirmed. A performance verification test was done for the electromechanical actuator system containing main model on a whole trajectory flying platform according to the data from wind tunnel measurement. The results show that the first order torsional frequency of clamped support control surface is 1 210.47 rad/s, and that of the transmission modal(consist of the control surface) is 1 148.17 rad/s, which is consistent with the theoretical result of 1 180.0 rad/s. The external loading verification of whole trajectory flying platform indicates that the actuator system meets the demand of performance index when the maximum hinge moment is 6.8 Nm, the elastic angle of control surface is 1.1°and the actuator maximum error of instruction from a tracking autopilot is ±0.1°.