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The formation of a new ocean basin provides a unique observational window into the structure and deformation of the oceanic lithosphere. This study offers a detailed 1‐D vertically polarized shear‐wave velocity model of the young Japan Basin by interpreting S receiver functions, seafloor Rayleigh wave ellipticities and phase velocities in a Bayesian trans‐dimensional framework. The models suggest a distinct discontinuity in the mid‐lithosphere. Additional analyses indicate that the upper layer is characterized by strong positive radial anisotropy, while the lower layer is more isotropic. We interpret that the upper layer was formed during the back‐arc opening at 20–15 Ma, where the olivine lattice‐preferred orientation (LPO) fabric induced by passive upwelling contributes to the positive radial anisotropy. The lower, less anisotropic layer may be solidified after the sudden cessation of the opening. Small‐scale convection (SSC) from such a major tectonic event could randomize the LPO enough to weaken radial anisotropy before cooling down the asthenosphere, leaving a radially anisotropic discontinuity in the present‐day mid‐lithosphere. The proposed layered evolution history of the lithosphere beneath the Japan Basin illuminates an important role of the small‐scale convection in modifying the structural fabrics of the asthenosphere in terms of radial anisotropy. Such an SSC‐induced radial anisotropy drop could also occur at the base of the lithosphere in regions with ongoing seafloor spreading and enhance the velocity drop of horizontally polarized shear waves. Thus, the role of SSC is non‐negligible in explaining the sharpness of the Gutenberg discontinuity detected by SS precursors beneath the oceanic lithosphere. Plain Language Summary: The formation of the oceanic lithosphere is associated with a relatively simple mantle convection process called seafloor spreading, but may also be affected by more complex, localized processes such as small‐scale mantle convection. To decipher the evolution history of the lithosphere of the Japan Basin, the Sea of Japan, this study collects earthquake waveforms from broadband ocean‐bottom seismometers and offers a detailed 1‐D seismic structural model beneath the Japan Basin by interpreting the multiple seismological observables in a trans‐dimensional Bayesian framework. Our seismic velocity model and associated analysis reveal that the oceanic lithosphere of the Japan Basin is seismically more complex than expected. The upper and lower parts of the lithosphere show distinct seismic anisotropy properties. We propose a layered evolution model for the lithosphere of the Japan Basin, in which small‐scale convection followed a normal seafloor spreading, and resulted in a structural discontinuity in the present‐day mid‐lithosphere. The proposed model highlights the role of the small‐scale convection in modifying the structural fabrics of the asthenosphere in terms of radial anisotropy. Key Points: We construct detailed 1‐D Vsv models of the Japan Basin by trans‐dimensional inversion of multiple observables extracted from ocean‐bottom seismometers recordsOur analysis reveals a mid‐lithosphere discontinuity arising from strong positive radial anisotropy in the upper lithosphereA layered evolution mode associated with small‐scale convection is proposed for the lithosphere of the Japan Basin [ABSTRACT FROM AUTHOR]