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This article offers the analysis of electromagnetic compatibility of high frequency switching power supply by finite element method of harmonic balance theoretically. Finite element method of harmonic balance is different from traditional time-domain finite element method and transient analysis method. Finite element method of harmonic balance produces solution using linear synthesis of sine function and represents wave figure using coefficient of sine function. It combines steady-state response of finite element method directly in frequency domain solution electromagnetic field. The experiment has proved finite element method of harmonic balance is generally more effective than traditional time-domain method.