The permanent magnet synchronous motor (PMSM) is widely used in ships under frequency conversion control system. The fluid flow performance and temperature distribution of the PMSM are difficult to clarify due to its complex structure and variable frequency control condition. Therefore, in order to investigate the fluid and thermal characteristics of the PMSM, a 50 kW PMSM was taken as an example in this study, and a 3-D coupling analysis model of fluid and thermal was established. The fluid and temperature fields were calculated by using finite volume method. The cooling medium’s properties, such a velocity, streamlines, and temperature, were then analyzed. The correctness of the proposed model, and the rationality of the solution method, were verified by a temperature test of the PMSM. In this study, the changing rheology on the performance of the cooling medium and the working temperature of the PMSM were revealed, which could be helpful for designing the PMSM.