We have proposed a new waveform inversion method to estimate a 2D S-wave velocity structure of deep sedimentary layers using broadband Love waves. As a preprocessing operation in our inversion scheme, we decompose earthquake observation records into velocity waveforms at periods of 1 s interval. Then, we verify an assumption of 2D propagations of Love waves with polarization features based on a principal component analysis to select the segments applied for the inversion. A linearized iterative inversion analysis for the selected Love wave segments filtered at period of every 1 s allows a detailed estimation of boundary shapes of interfaces over the seismic bedrock with an S-wave velocity of approximately 3 km/s. We demonstrate the technique’s effectiveness with applications to observed seismograms in the Kanto plain, Japan. Differences between the estimated and existing structural models are remarkable at basin edges. A regional variation of the near-surface S-wave velocities in our model is similar to a distribution of surface geological classifications. Since a subsurface structure at a basin edge strongly affects earthquake ground motions in a basin with generations of surface waves, our method can provide a detail model of a complex S-wave velocity structure at an edge part for a strong ground motion prediction.