Deep space exploration has an extremely high requirement for beam pointing accuracy of the large reflector antenna fed by a beam waveguide system. Beam pointing error compensation is of great importance when the reflector is deformed by inevitable external loads. This study introduces an innovative compensation method for such large beam waveguide reflector antennas utilizing an adjustable ellipsoidal mirror in the beam waveguide system. Initially, the effect of the ellipsoidal mirror’s position deviation on the beam waveguide system’s outgoing focus is analyzed. Subsequently, an equivalent single reflector system for the dual reflector system of the beam waveguide reflector antenna is considered, and the derivation of the focus position deviation for the single reflector caused by the position deviation of the beam waveguide system’s outgoing focus is derived. Then, an electromechanical coupling model (EMCM) is formulated, incorporating both the reflector deformation and the ellipsoidal mirror’s position error. Finally, with the assumption of adjustability of the ellipsoidal mirror, the study explores the beam pointing error compensation problem based on the EMCM in scenarios of reflector deformation. This paper presents a case study on a 35 m aperture beam waveguide reflector antenna. The results demonstrate that the proposed EMCM achieves high accuracy in calculating the main beam direction, thereby validating the effectiveness of the proposed beam pointing error compensation method for large antennas.