A satellite dedicated for quantum science experiments, has been developed and successfully launched from Jiuquan, China, on August 16, 2016. Two new optical ground stations (OGSs) were built to cooperate with the satellite to complete satellite-ground quantum experiments. OGS corrected its pointing direction by satellite trajectory error to coarse tracking system and uplink beacon sight, therefore fine tracking CCD and uplink beacon optical axis alignment accuracy was to ensure that beacon could cover the quantum satellite in all time when it passed the OGSs. Unfortunately, when we tested specifications of the OGSs, due to the coarse tracking optical system was commercial telescopes, the change of position of the target in the coarse CCD was up to 600μrad along with the change of elevation angle. In this paper, a method of reduce alignment error between beacon beam and fine tracking CCD is proposed. Firstly, OGS fitted the curve of target positions in coarse CCD along with the change of elevation angle. Secondly, OGS fitted the curve of hexapod secondary mirror positions along with the change of elevation angle. Thirdly, when tracking satellite, the fine tracking error unloaded on the real-time zero point position of coarse CCD which computed by the firstly calibration data. Simultaneously the positions of the hexapod secondary mirror were adjusted by the secondly calibration data. Finally the experiment result is proposed. Results show that the alignment error is less than 50μrad.