The EPS motor will be over-heated if large current lasts for a long time, which will decline the performance of EPS motor and even lead to irreparable damage. So the over-temperature protection control should be conducted in order to protect the components of EPS system, especially the durability of EPS motor. In this paper, the motor temperature was estimated according to the environmental temperature and the current of motor armature, and then the EPS assist current was limited based on the estimated temperature of motor to ensure that the EPS motor had a good working condition. So the over-temperature protection control for motor can be realized without increasing the EPS system components. Finally the control strategy for over-temperature protection was conducted in a vehicle with EPS system and its performance was verified.