Abstract: The Cyclotron Injection System of the Wuwei Heavy Ion Medical Machine consists of a cyclotron that has a weight more than 50 tons, an ion source and some auxiliary facilities. As the ion source and the cyclotron use one girder and have a very tight construction, it is difficult to install and align the system. By the aid of a laser tracker and a three-dimensional control network, through step by step survey and alignment from bottom to top, our method improves the work efficiency of alignment and guarantees a 0.10 mm deviation for each finally installed magnet in each direction. The results are better than the installation precision demands of the Heavy Ion Medical Machine. Currently, the cyclotron injection system has been successfully commissioned and the performance is proved well, and some indexes are better than the design targets, which also verify that the method used for this system has a high accuracy and feasibility.