In order to improve the tracking performance of the laser communication tracking system and enhance the anti-disturbance capability of the system, a single-detector composite axis control method based on Kalman filter was proposed. Firsty, the principle of the single detector composite axis system was analyzed, and the feasibility of the decoupling algorithm was verified by the error transfer function. Then in order to improve the impact of miss distance and reduce the real-time processing requirements of the detector, an adaptive Kalman filter algorithm was proposed. Finally, according to the rotation transformation relationship between the detector coordinate system and the fast steering mirror coordinate system, the decoupling matrix of the coarse and fine system was calculated, and a desktop experimental system was built to verify the principle. With the condition of 0.1 Hz low frequency disturbance, the relative displacement of the fine tracking system will not exceed the critical value of the mirror deflection angle, and the tracking error will decrease from 2.54 μrad to 0.86 μrad. The experimental results show that the decoupling control can improve the tracking accuracy and enhance the anti disturbance ability of the system. It has a certain guiding significance for the practical application in the future engineering.