For finding better analysis method, Hilbert-Huang transform (HHT) was applied as a tool of time-frequency analysis in Magnetotelluric (MT) signals processing. By means of Wavelet transform (WT) and HHT, a practical MT signal is analyzed and its results are compared from the fields of decomposition and reconstruction, de-noising, time-frequency analysis. From the results, it can be drawn that HHT method is more adaptive than WT analysis in analyzing non-stationary MT signals and will has a wide application on MT signals processing.