Abstract: In order to improve the disturbance rejection rate and time characteristics of a seeker, an optimization design of seeker control system in the inner-loop and outer-loop respectively based on the disturbance rejection rate is proposed. The mode of disturbance rejection rate of seeker is established and the disturbance rejection rate function is derived. The relationship between the disturbance rejection rate and inner and outer loops is analyzed. The amplitude margin and phase margin constraints of seeker are converted into the stable domain of the control parameters by the amplitude-phase test method. The optimized design parameters of seeker are obtained by optimization the disturbance rejection rate objective function of in the stabilizing loop and time response characteristics objective function in the optimal tracking loop respectively, within the stable region. The simulation results show that the optimized seeker control system has better time domain performance and improves the disturbance rejection rate.