In order to improve the disturbance isolation degree for space optical communication Pointing, Acquisition, and Tracking(PAT) system, a novel control method based on disturbance observer was proposed. Firstly, according to the structure analysis of PAT system, the simplified system model was gained and then the disturbance was observed from the position of the motor and the laser spot by disturbance observer. Finally, the equivalent amount of disturbance compensation was added to the integration points in front of the current loop. The simulation results of fine tracking system show that compared with the traditional PD controller, adding the disturbance observer can improve the disturbance isolation degree at almost all frequencies before the motor current saturates, and the optimal situation has reached 28.2 dB. Meanwhile, this method has strong robustness; the disturbance isolation degree still increases by at least 1 times than not using the disturbance observer when there are 15% changes for the system physical parameters. The proposed control method greatly improves the disturbance isolation degree for PAT system and is of certain reference value to the wide range and high dynamic precision photoelectric tracking system.