A new wavelet energy transfer function spectrum(WETFS)method was proposed in this study to remove frequency contamination of earthquakes from wavelet spectrum of structural responses in identifying fre-quency variation of structures.First,wavelet spectrums of earthquake excitation and structural response were integrated along time respectively to get wavelet energy spectrum of earthquakes and seismic responses.Then the WETFS was defined by dividing wavelet energy spectrum of earthquake excitation by that of structural re-sponse.The ridge on WETFS just represented the variation of structural frequencies.This method and the tra-ditional wavelet method were both applied on frequency identification of one 6-story masonry apartment build-ing.The seismic responses of this building during series of aftershocks of Wenchuan earthquake were measured and structural frequencies were identified to decrease remarkably during two aftershocks.The results of the two methods indicate that the WETFS method can identify variation of structural frequency accurately without con-tamination of earthquake excitation.