When fault occurs in transmission line, due to the discontinuity of the wave impedance, the reflection phenomenon of the fault traveling wave will form a series of aliased natural frequency spectrum, thus effectively and accurately extracting the traveling wave natural frequency from the aliasing phenomenon as the fault Ranging the primary problem. Therefore, the singular value differential spectrum theory is used to classify the original signal, which can not only reduce the noise interference, but also can extract the signal to different frequencies, reduce the spectrum mixing phenomenon, and adopt the probability estimation algorithm based on harmonic model to accurately identify the inherent frequency. By PSCAD simulation, this method can extract the natural frequency of the traveling wave accurately from the spectral mixture and realize the fault location of the power grid.