The high frequency isolated quasi Z-source inverter is a new type of inverter, which is suitable for photovoltaic generation system because of its high lift to voltage ratio, transient bridge direct access and electrical isolation.With the increase of its power density, the working frequency of its semiconductor switching devices is increasing. Switching devices in high-frequency states generate a large amount of electromagnetic noise, affecting the normal operation of surrounding electrical equipment and threatening the stability of the power grid. For the optimization of electromagnetic compatibility of high frequency isolation quasi Z-source inverter, using pulse width modulation (PWM) chaotic modulation technology, put forward using Chen multi-scroll chaotic system and traditional PWM are combined, using the new PWM control technology can inhibit electromagnetic interference (EMI) from the noise source, effectively reduce the high frequency isolation quasi Z-source switch frequency and its harmonics noise power, and optimize the total harmonic distortion (THD) of the output current by analyzing the chaotic modulation coefficient. Finally, the correctness of the theory is verified by Saber simulation and circuit test. This paper can provide guidelines for the electro magnetic compatibility (EMC) design of the high frequency isolated quasi Z-source inverter and provide the theoretical basis for the EMI optimization design of the power electronic system.INDEX TERMS High frequency isolation quasi Z-source inverter, chaotic pulse width modulation (PWM) technology, multi-scroll chaos of Chen system, electromagnetic interference (EMI), total harmonic distortion (THD).