Abstract With the development of accelerator technology, the scale of accelerators is becoming larger, ranging from hundreds of meters to several kilometers. For stable operation of accelerators, high-precision alignment, positioning, and installation are crucial. Installing all equipment inside the tunnel poses safety risks as personnel would be in a closed environment with potential radiation exposure for prolonged periods. To address the challenges of long adjustment and maintenance periods inside the tunnel due to the installation of equipment for large-scale accelerators, most accelerator devices under construction or in research have pre-alignment assemblies. Each assembly consists of a certain number of magnets distributed on girders. The magnets in one unit are pre-aligned with high precision in the laboratory and then transported to the tunnel. Aligning the entire magnet girder can significantly improve installation efficiency inside the tunnel. To meet the pre-alignment accuracy requirement of 10 μm in the horizontal and vertical directions for the magnet units in the high energy photon source (HEPS) storage ring, a system for high-precision pre-alignment of accelerator units using four total stations for angle observation has been designed in this paper. By employing different instrument layout configurations and incorporating reliable distance benchmarks, high-precision pre-alignment of the magnet are achieved. By arranging targets and utilizing recognition for automatic targeting, real-time point calculations during pre-alignment enhance efficiency. Subsequently, based on this system, pre-alignment simulation calculations and experimental verification of eight magnet focusing–defocusing units in the HEPS storage ring are conducted and ultimately realizing the 10 μm transverse and vertical pre-alignment measuring error within the units. This method, based on high-precision measurements in a small-scale space, reduces the period required for personnel on-site and improves pre-alignment efficiency. It also provides a reference for pre-alignment of multiple magnet units in large accelerators such as the Southern Advanced Photon Source and Circular Electron Positron Collider.