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This work proposes a frequency-domain EMI prediction model for common mode (CM) and differential mode (DM) noises for the purpose of designing EMI filters before the system construction. The parameters in the model can be extracted from system detail switching model or measured from the real system. The Double Fourier Integral Transformation (DFIT) method is used to calculate the noise sources in the model. When the system topology modulation method and modulation index is fixed, the system EMI noise can be predicted from the calculation of the equivalent model. Verifications are carried out through simulation and experiment system by comparing the calculated EMI spectrums and simulated and measured EMI spectrums. Based on the proposed model, this paper also proves that the resonances in EMI noise propagation path will have a significant impact on the EMI filter design for DC fed motor drive system with long cables.