The invention relates to a beacon optical axis precision positioning system in an atmosphere laser communication system, which is characterized by comprising an optical receiving antenna (1), a vibrating mirror (2), a dispersion prism (3), a Hartmann sensor optical axis precision positioning unit (4), a vibrating mirror controller (5), a lens (6) and a common CCD camera (7). To realize the real-time correction of the pointing direction of a beacon optical axis, the beacon optical axis precision positioning system detects a beacon light beam by a Schack Hartmann sensor with microlenses array and reconstructs a real-time wavefront image by a Zernike Polynomial mode method, thereby resolving the real pointing direction of the beacon optical axis of the atmosphere laser communication system and achieving final optical axis positioning precision exceeding 2 mu rad. If a common CCD positioned at a receiving end needs to obtain same resolution ratio and measuring precision, an optical systemof the common CCD has large volume and heavier weight; in addition, compared with the traditional platform, the invention has obviously reduced volume and weight, thereby effectively meeting the requirement of future space laser communication for the light type of an onboard platform.