To address the significant heat generation issue that encountered during the operation of permanent magnet synchronous motors (PMSM) in new energy vehicles, alongside the challenge of ineffective heat dissipation caused by the constrained installation space of the motors. This study uses a 90 kW permanent magnet synchronous motor as the subject of investigation. Through electromagnetic design analysis, the performance of the motor under both no-load and loaded conditions was evaluated respectively, and the cogging torque was optimized through segmented inclined electrodes. On this basis, this paper conducts a comparative analysis of the impact of various waterway structures and water flow velocities on the motor’s temperature rise under the condition of the same heat dissipation area. Through the optimization of the water cooling system design, an analysis of the impact of various parameters on heat transfer efficiency, and the proposal of effective heat dissipation strategies, the motor’s temperature is maintained within a reasonable range during prolonged operation, thereby improving its overall stability and reliability.