We investigate layering structure in the mantle beneath Japan using ScS reverberation waveforms of two recent large deep events in the northwest Pacific. We estimate regional variation of the elastic and anelastic structure of the mantle as well as properties of the major velocity discontinuities by modeling broadband seismograms recorded at two dense networks, J-Array and FREESIA. The 660-km discontinuity is the deepest in the region where the stagnant subducting slab in the transition zone is tomographically imaged, but the subsidence is of similar to 10 km, much smaller than previous estimates with SS precursors. No significant elevation is detected for the 410-km discontinuity.