The azimuth axis drive and control of large telescopes based on Segmented Arc Permanent Magnet Synchronous Motor (SAPMSM) is a current research hotspot, and issues such as unknown parameters and external interference are important factors affecting its tracking accuracy. This paper proposes a SAPMSM perturbation suppression strategy for large telescopes based on port-controlled Hamiltonian (PCH) theory. In this study, the Hamiltonian mathematical model of SAPMSM is established and the current controller of the SAPMSM is designed to reduce harmonics by configuring the required interconnection and damping matrix. In order to further improve the accuracy and anti-disturbance performance of speed feedback, a Generalized Proportional Integral Observer (GPIO) is selected for total disturbance observation, estimation and compensation. The experimental results indicated that the algorithm proposed in this paper has lower harmonic content in the phase current of the SAPMSM, which can ensure good position tracking ability and anti-interference performance of large telescopes.