With the rapid development of technology, motors have drawn increasing attention in aviation applications, especially in the more electrical aircraft and all electrical aircraft concepts. Power weight ratio and reliability are key parameters for evaluating the performance of equipment applied in aircraft. The temperature rise of the motor is closely related to the reliability of the motor. Therefore, based on Taguchi, a novel multi-objective optimization method for the heat dissipation structural design of an electro-hydrostatic actuator (EHA) drive motor was proposed in this paper. First, the thermal network model of the EHA drive motor was established. Second, a sensitivity analysis of the key parameters affecting the cooling performance of the motor was conducted, such as the thickness of fins, the height of fins, the space of fins, the potting materials and the slot fill factor. Third, taking the average temperature of the windings and the power weight ratio as the optimization goal, the multi-objective optimal design of the heat dissipation structure of the motor was carried out by applying Taguchi. Then, a 3-D finite element model of the motor was established and the steady state thermal analysis was carried out. Furthermore, a prototype of the optimal motor was manufactured, and the temperature rise under full load condition tested. The result indicated that the motor with the optimized heat dissipating structure presented a low temperature rise and high power weight ratio, therefore validating the proposed optimization method.