Permanent magnet of permanent magnet synchronous motor was limited by the thermal constraints and could not operate in high temperature environment. Therefore, it was necessary to reduce the eddy current loss on permanent magnet so as to lower the temperature on permanent magnet. In view of the long calculation time of the eddy current loss estimation of permanent magnets by finite element method (FEM) and the difficulty of achieving the same accuracy as the FEM when using the analytical method, the hybrid analyticalFEM to estimate the eddy current loss of permanent magnets was adopted, and the reaction field of eddy current was taken into account. When simulating the rotation of motors, there was no need to repeat the triangle mesh division. By using MATLAB software, the hybrid analyticalFEM was compared with the Galerkin FEM, which reduced the number of triangles. The characteristic of the end effect and the skin effect of the eddy current losses on the permanent magnet were validated. The hybrid analyticalFEM could ensure the accuracy and reduce the simulation time.