In view of the polarization maintaining problem in quantum communication using satellites,the atmospheric scattering and the relative motion between satellite and ground station which have impact on the photon polarization states in satellite quantum communication were researched. The influence on quantum bit error rate of the system caused by alignment error and phase delay was simulated and analyzed. The existing polarization compensation scheme that combines the BB84 protocol and half wave plate rotating has a defect that cannot communicate in the process of compensation. A new scheme was proposed to overcome the defect by joining the advanced compensation before the alignment. The result is that the polarization error can be compensated to zero and the safe and reliable quantum communication using satellites can be realized. And it’s convenient to realize because the scheme only need to add a half wave plate on the original system.