Active-short-circuit and locked-rotor modes are common abnormal operations in new energy vehicles. The IGBT junction temperature measurement for these two operating conditions is a challenging problem due to the unexpected large current and the asymmetric operation of semiconductor chips. In addition, different cooling flow rates have a significant influence on the heat dissipation, which will also have an impact on the building of the thermal model. Based on these difficulties, a modified Foster thermal network under active-short-circuit and locked-rotor modes has been presented considering different cooling conditions. The power loss models of the semiconductor chip under abnormal conditions are developed and a modified Foster thermal network based on the NTC temperature sensor is proposed. The model can be adapted to different cooling conditions since the thermal impedance fluctuates slightly at different cooling flow rates. The proposed thermal model is verified with inverter application under active-short-circuit and locked-rotor modes and the experimental performance shows good accuracy compared with the infrared camera measurement results.