To investigate the dominant deformational patterns and stress conditions in the upper crustal structure of the Kinki region, southwest Japan, we constructed a high-resolution 3D azimuthal anisotropy model to a depth of ~ 11 km. We used 6-month-long ambient noise data recorded by the densely distributed permanent and temporary stations. From this dataset, cross-correlations were retrieved. We then obtained a 3D isotropic velocity model by inverting Rayleigh wave dispersion data, followed by a direct joint inversion for both 3D azimuthal anisotropy and additional isotropic velocity perturbation. The resolved 3D azimuthal anisotropy reveals significant contrasts of anisotropy across the Kinki region. The southern part of the Kinki region shows predominantly NE-SW-trending fast axes, ascribed to fossil anisotropy. The fast axes in the northwestern Kinki region are consistent with the direction of the maximum horizontal compressional stress and the principal strain rate axes, suggesting that the observed anisotropy is mainly stress-induced. On the depth profile of the anisotropy, we found depth-dependent variation of azimuthal anisotropy. There exist a significant consistency between the anisotropy observed beneath 3 km depth and the dense distribution of earthquake hypocenters (≥4 %). This interrelationship between anisotropy and seismicity demonstrates that the observed anisotropy could be linked to local crustal stress or fractures relevant to earthquake ruptures. Our high-spatial resolution 3D anisotropy model therefore contributes towards understanding the locations and features of the seismicity region.