This paper discusses the target tracking problem with high-frequency disturbance rejection demand for the tip-tilt mirrors component in electro-optical systems, where the mechanical vibration disturbances always exist near the system’s resonance. After analyzing the influence of resonance to the tracking performance, a modified two degrees of freedom control scheme is proposed. Specifically, utilizing the decoupling capacity, the feedback control without resonance compensation is designed to attenuate system resonance’s neighboring disturbances, and a feedforward controller is added to make up for the sacrifice in tracking performance. As the tracking performances are difficult to be fused and judged, the parameters’ tuning problems are skillfully translated into a proportion optimization problem with a genetic algorithm. By this method, the controller can be finely designed and tuned to match particular systems and meet the performance demands. A series of simulations and experiments illustrate the effectiveness of this new 2-DOF control scheme.