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In order to economize power energy, the high voltage inverter is used widely in the production of industry and agriculture. The security and reliability problem is more and more important. However, the high voltage inverters controller system can check the base problem, such as under voltage protection, open-phase protection, IGBT over current, IGBT over voltage, IGBT over heat etc. Therefore, it is very necessary to research a deep fault diagnosis system. The paper gives a wavelet transform method of the fault diagnosis of high voltage inverter, and introduces the hardware structure and software flow of the fault diagnosis system.