The composition and control structure of fine tracking system of free space laser communication are briefly described. The error sources of the beacon positioning of fine tracking detector using centroid algorithm of the acquisition, tracking and pointing system are analyzed. And the Fourier frequency domain of the beacon positioning process of fine tracking detector is analyzed too. The theoretical scheme for eliminating the systematic error of centroid algorithm is derived, that is, the product of the beacon light wavelength and the F number of the fine tracking system need to be larger than the pixel size of the fine tracking detector. The selection process of the key parameters in the implementation of the fine tracking system is analyzed，and considering the coupling relation of system parameters of fine tracking system, in order not to lose fine tracking field of view, the optimization of fine tracking system by adding aperture diaphragm before fine tracking detector lens is implemented for eliminating the systematic error of centroid algorithm. The theoretical calculation and experimental results show that when the aperture diameter is less than 9.32 mm, the relative aperture of the fine tracking system is less than 0.045, and the fine tracking error is only 0.03 pixel, and the tracking accuracy is improved by 1.9 times.