[Objective] The canned permanent magnet synchronous motor (CPMSM) is widely used in critical fields such as chemical processing, nuclear power, and medical applications due to its high power density, superior efficiency, and excellent dynamic performance. However, research on the impact of batch-produced permanent magnet performance variations on long-term motor stability remains insufficient. Therefore, this study aims to analyze the influence of permanent magnet variations on CPMSM performance and reveal its multi-physics field coupling mechanisms. [Methods] Firstly, a load backs electromotive force-based real-time detection method for permanent magnet magnetic properties was proposed, enabling dynamic post-assembly monitoring without additional sensors. Then, the influence of permanent magnet performance variations on CPMSM electromagnetic fields, temperature distribution, and shield-can thermal stress/deformation was analyzed using finite element models. Finally, experimental validation of the proposed method was subsequently conducted. [Results] The results demonstrated that when compared with the N30-grade, the motor with N38-grade permanent magnets exhibited a 2.56% difference in power factor, a 1.76% difference in efficiency, a 5 ℃ difference in winding temperature, and a 5.82 ℃ difference in casing temperature. [Conclusion] A decline in the magnetic performance of permanent magnets leads to nonlinear deterioration in motor performance metrics, and the performance difference is solely related to the quantity of permanent magnets, independent of their distribution. This study provides theoretical references for the optimized design of CPMSM, the evaluation of permanent magnet deviation impacts, and the enhancement of reliability in harsh environments.