Abstract: The function of the empirical mode decomposition and margin spectrum of the Hilbert-Huang Transform (HHT) is applied to the analysis of geo-electric data observed by the Xiji station, Tongzhou district of Beijing. The recorded data is remarkably disturbed by theBeijingsubway, making the data utilization rate very low. The effects of the subway on the data has been analyzed. The result shows that, when the recording track goes parallel to the subway line, the recorded data would be most severely affected. Making use of the function of empirical mode decomposition of HHT can eliminate most subway disturbance and reduce its influence to the least. In addition, the analyzed result of margin spectrum indicates that the energy of the subway disturbance is lower than that of normally observed geo-electric field.