Seismic inversion is one of the key techniques used for reservoir characterization. Depth-domain seismic inversion eliminates the cumulative errors associated with depth-to-time and time-to-depth conversions, thus providing geologists and reservoir engineers with an intuitive basis for geological interpretation. The method has received increasing attention in the field of reservoir characterization. Extracting accurate depth-domain seismic wavelets is a prerequisite for successful depth-domain seismic inversion. However, the depth-domain wavelet is velocity-dependent and exhibits significant non-stationarity, which leads to the failure of seismic wavelet estimation methods based on the stationary convolutional model. To this end, we propose a modified wavenumber-domain unscaled S-transform (MWUST) method to accomplish accurate estimation of depth-domain seismic wavelets. The proposed method enhances the accuracy of wavenumber components by removing the linear wavenumber-dependent term from the S-transform. Furthermore, it introduces slope and intercept parameters to improve the depth resolution at low wavenumbers, thereby yielding a more reliable depth–wavenumber spectrum. Subsequently, the relationship between the non-stationary depth-domain seismic wavelet and the depth–wavenumber spectrum is established, allowing for the accurate extraction of non-stationary wavelets under the assumption that the depth-domain reflectivity is a random sequence. Synthetic and real data applications have been used to verify the effectiveness of the proposed method.