Abstracts High-power insulated gate bipolar transistor (IGBT) modules are widely used in power electronic systems, their system reliability is received more and more attention. The junction temperature of power devices is an important factor affecting reliability of power electronic systems. For electric vehicle applications, this paper proposes a method of junction temperature estimation and over temperature protection is used for electric vehicle's IGBT power modules. According to two junction temperature estimation methods, one is based on the thermal impedance model of IGBT modules, and the other is based on the relationship between the negative temperature coefficient (NTC) thermistor temperature and the chip temperature inside modules, two estimated junction temperatures can be obtained. Under different working conditions, the two estimated junction temperature ratios are adjusted to obtain an optimal estimated junction temperature. Based on the junction temperature estimation, several temperature thresholds are set. When the temperature reaches the threshold value, the motor drive control is used to perform effective over temperature protection to prevent the IGBT modules of the electric vehicle inverter from being ineffective due to the excessive junction temperature and resulting in the loss of vehicle power.