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The application of very fast image detectors to the fine tracking system of free space optical (FSO) communication has been demonstrated in several projects. In the near surface of the earth, the influence of the atmosphere on the optical communication system must be considered. The optical communication system must be designed to be able to suppress the influence of atmospheric turbulence. The authors have used the high-speed CMOS image sensor for the fine tracking system of 15 km FSO communication demonstration. In this study, the authors present the atmospheric influence on the fine tracking detector, and find out the tracking algorithm for the fine tracking detector to detect the centre of the received spot. On analysis of atmosphere turbulence influenced and the experiment data, the authors find that using centroid algorithm in the fine tracking system is better than the centre of mass algorithm. They proposed a new centroid algorithm in the fine tracking system and use this algorithm in the demonstration system. They found it can minimise the atmosphere turbulence influence.