In the single terminal fault locating method of transmission line based on traveling wave natural frequency, the accuracy of extracting primary natural frequency is the key to caring out to pinpoint trouble spots in. Currently, wavelet transform and MUSIC method are commonly used for extracting primary natural frequency. Wavelet analysis is influenced by the selected wavelets and the parameters’ selection greatly impacts spectral estimation in MUSIC, which can’t solve this problem well. A new single ended fault location method of extracting faulted line natural frequencies is described. The traveling wave signal is decomposed by EEMD and orthogonal process is made with ICA method to suppress the WVD''s problem of cross-term, and then each component of WVD is converted and superimposed to obtain the natural frequency spectrum orthogonal. Then the global primary natural frequency is obtained considering the fundamental and harmonics. Simulation experiment by EMTDC confirms the feasibility and accuracy of the proposed algorithm under different fault types, fault distance, transition resistance and noise situation. This work is supported by National Natural Science Foundation of China (No. 60974125).