In order to ensure the reliability of power electronic devices, it is necessary to make a comprehensive knowledge of the thermal analysis for power devices. However, the junction temperature calculation of IGBT is an enormous challenge in thermal analysis. First of all, in order to analyze its characteristics and calculate junction temperature accurately, the systematic and thermal model is established in MATLAB. The parameters of the model are easy to obtain and the calculation process is simplified. Then, through ANSYS Icepak, the comparison is conducted with or without consideration of transverse heat conduction (THC). The results show that the consideration of THC can make calculation become more accurate. Finally, in order to verify the junction temperature estimation method for a two-level voltage source inverter (2L-VSI), through the simulation analysis of the model, it is concluded that the calculation error of the model considering THC is smaller, and the parameters are easy to obtain, which provides theoretical help for junction temperature calculation.