Abstract: The high energy climbing segment of the Wuwei Heavy Ion Medial Machine has a vertical span of about 18 meters. Due to the suspended installation of oversized and overweighted components, the small installation space and lack of straight sight conditions, the position and angle of the placed magnet is different from the magnet in ground situation, which brings big challenges to the installation alignment. By the aid of a laser tracker and a three-dimensional control network, through multiple coordinate conversion, we explored a new method to eliminate the deviation brought by adjusting the angle of magnet in the climbing segment. This method has effectively improved the efficiency of installation alignment and guaranteed a deviation below 0.10 mm for each finally installed magnet in each dimension. The results are better than the installation precision demands of the Heavy Ion Medical Machine, which provides a strong guarantee for advancing the overall installation process.