Identification of different wave types in a seismogram is an important step for the understanding of wave propagation phenomena. Because in most seismograms, different types of waves with different frequencies may appear simultaneously, separation of waves is more effectively achieved when a time–frequency analysis is performed. In this work, we propose a new time–frequency analysis procedure to identify and extract Rayleigh and Love waves from three‐component seismograms. Exploiting the advantage of the absolute phase preservation by the Stockwell transform, we construct time–frequency filters to extract waves based on the normalized inner product (NIP). Because the NIP is the time–frequency counterpart of the correlation, Rayleigh and Love waves can be identified depending on the NIP between the Stockwell transforms of the horizontal and vertical displacement components. The novelty and advantage of the proposed procedure is that it does not require specifying a priori the direction of propagation of the surface waves, but instead such direction is determined. Furthermore, it is shown that the NIP is a more stable parameter in the time–frequency domain when compared to the instantaneous reciprocal ellipticity, and thus it avoids smoothing (and with it, altering) the data. The procedure has been successfully tested with real signals, specifically to extract Rayleigh and Love waves from seismograms of one aftershock of the 1999 Chi‐Chi earthquake. With the proposed procedure, we found different directions of propagation for retrograde and prograde Rayleigh waves, which might suggest that they are generated by different mechanisms.