With the rapid development of electric vehicles and integrated electric drive systems, the power density of permanent magnet synchronous motors (PMSMs) continues to increase, leading to a significant rise in operating temperatures. Although efficient cooling systems can effectively reduce these temperatures, changes in structures often result in increased motor costs, thereby affecting efficient operation. To verify the effectiveness of motor cooling structures, this paper proposes an evaluation method for PMSMs’ cooling structures that takes motor costs into account. By considering energy consumption and the magneto-thermal bidirectional coupling principle, the operational cost of the motor is calculated. Combined with the manufacturing cost, a comprehensive evaluation index is established to assess motors with different cooling structures. The research results indicate that the spray cooling structure improves the comprehensive economic efficiency by up to 5.3% and 1.6% compared to the water jacket cooling structure. This demonstrates that the spay cooling structure effectively ensure efficient motor operation, and proving the effectiveness of the method proposed in this paper, with providing a basis for designing efficient PMSM cooling structures.