With the aim to attenuate the effect of wind load disturbance on the tracking precision and the life-span of a large deep space observatory antenna, this paper proposed a wind disturbance rejection servo system. As disturbance observer can improve the system performance, the mechanism of electrical motor was utilized to simplify the design process. The feedback channels of current and speed control as well as load impact were regarded as parts of the total disturbance, and the lags in the feed-forward channels were approximated by their steady gains respectively. Therefore, the required order of the extended state observer, which was employed to estimate the total disturbance, including the wind load torque and other uncertain mechanical dynamics, could be substantially reduced. Then, the total disturbance was compensated by the observer. Furthermore, the limit cycle was eliminated in the presence of friction according to the describing function method. Finally, mathematical simulations and experiments were carried out. In the experiment, the overshoot is reduced by 34% and the capacity of gust rejection is increased by 60% ,respectively, as compared with that of traditional equipment, while the tracking precision is also raised significantly. The objective of rejecting the wind gust disturbance for the large deep space observatory antenna system can be achieved by using the proposed method.