Purpose <p>The BEPCII upgrade project aims to enhance the collider’s energy and luminosity. This necessitates the replacement of the BESIII detector and its superconducting magnet within the complex and spatially constrained interaction region (IR). This paper addresses the challenges of installing and aligning the new final-focus superconducting magnet, which is subject to significant deformation from magnetic forces.</p> Methods <p>A detailed installation procedure for the interaction region equipment, particularly the vacuum chambers inside BESIII and the movable platform, was developed. Finite element analysis was performed to simulate the deformation of the superconducting magnet and its support structure under combined gravity and magnetic loads. A comprehensive alignment methodology was established, encompassing the fiducialization of the magnet’s mechanical and magnetic axes, a pre-alignment strategy for the magnet assembly, and a precise tunnel alignment procedure utilizing a laser tracker.</p> Results <p>The installation of all interaction region equipment was successfully completed. The deformation analysis provided critical data for compensating the magnet's position; the results showed a vertical deformation difference of 0.826&#xa0;mm at one end of the magnet after applying magnetic forces. The fiducialization and magnetic measurement alignment achieved an accuracy better than 0.08&#xa0;mm. The final alignment of the superconducting magnet in the tunnel was achieved with transverse and vertical offsets within 0.05&#xa0;mm of the pre-corrected theoretical coordinates.</p> Conclusion <p>The formulated installation procedure and the precision alignment method, which effectively compensated for operational deformations, proved successful for the BEPCII upgrade. The strategies described ensure the positional accuracy of the superconducting magnet during operation and provide a valuable reference for similar accelerator upgrade projects involving complex interaction region integrations.</p>