To overcome the adverse effect of complicated resonant vibration resulting from the OE-radar integrative measuring system on a servo unit, a hybrid compensating method combined an adaptive notch filter and the feedback of observer filtering was proposed to restrain the resonant vibration. Firstly, the resonant characteristics of the system were analyzed according to the mechanical structure and tested frequency properties. It indicates that there are three kinds of primary resonant modes in the system, which is the radar antenna resonance, radar cabin resonance and the antenna high-order and bearing coupling resonance. The rule of resonant characteristics varying with an elevation angle was also obtained. Then, a compensating method to the complicated resonant vibration was discussed. The adaptive notch filter in series was applied to compensation of the radar antenna resonance and the radar cabin resonance, and the feedback of the Kalman observer filtering was used to restrain the antenna high-order and bearing coupling resonance. Experimental results indicate that all kinds of resonances are restrained effectively by the hybrid compensating method, the velocity close-loop bandwidth of servo unit is up to 115 rad/s, and the transient time of step response is 0.35 s. The method proposed can satisfy the system requirements for high bandwidth and stabilization.