As the power source of electro-hydrostatic actuator (EHA) system, high speed permanent magnet motor has small heat dissipation area and large heating power, which can easily lead to an extremely rapid temperature increase. For the heating problem, this paper researched the calculation of power losses and thermal modeling of EHA motor, in order to predict the temperature rise. First, heat transfer analysis for the motor is presented in this paper in which the heat flows inside and outside the motor is described precisely. Second, the power losses are calculated by Joule's law, Bertotti empirical formula and viscous friction theory respectively. Then, a 3D steady thermal model is developed with FEM, and validated by test results. Finally, the temperature rising behaviors of the motor and coolant oil are discussed through simulation results. The results show that the overall temperature rise goes down at first and then increase slightly with respect to the speed; the maximum temperature drop can up to 5 °C when outside air velocity increasing by 5 m/s. Besides, increasing the flow of coolant oil can remarkably reduce the temperature rise.