In this paper, a mathematical analysis of the EMI (Electromagnetic Interference) for a 20 kHz/10 kV capacitor charging power supply in frequency-domain is presented, and a related circuit model considering the transient switching interference is proposed. Due to the high working frequency and the device-switching transitions, the conducted EMI caused by the charging circuit which includes the harmonics of grid frequency, working frequency and device-switching transition frequencies. Thus under certain working situations or loads parallel power supply, the interference may cause charging failure. To solve this problem, a high frequency transformer modeled with stray capacitances and an approximation of the device-switching transition is applied in the Spice-based simulation model, and a mathematical analysis in frequency-domain is presented.