Research interest in the Kinki region, southwestern Japan, has been aroused by the frequent occurrence of microearthquake activity that do not always coincide with documented active fault locations. Previous studies in the Kinki region focused mainly on deep, large-scale structures and could not efficiently resolve fine-scale (~10 km) shallow crustal structures. Hence, characterization of the upper crustal structure of this region at an improved spatial resolution is required. From the cross-correlation of the vertical components of the ambient seismic noise data recorded by a densely-distributed seismic array, we estimated Rayleigh wave phase velocities using a frequency domain method. Then, we applied a direct surface wave tomographic method for the measured phase velocity dispersion data to obtain the 3D S-wave velocity model of the Kinki region. The estimated velocity model reveals a NE-SW trending low-velocity structure coinciding with the Niigata-Kobe Tectonic Zone (NKTZ) and the active Biwako-seigan Fault Zone (BSFZ). Also, we identified fine-scale low-velocity structures coinciding with known active faults on the eastern side of the NKTZ, as well as sets of low-velocity structures across the Tanba region, that may be attributable to the weathering effects or activity of unidentified concealed fault zones. Furthermore, sedimentary basins manifest as low-velocity zones extending to depths ranging from ~1.5 to 2 km, correlating with those reported in previous studies. Our results therefore contribute towards fundamental understanding of earthquake faulting as well as tectonic boundary and will be useful for hazard assessment and disaster mitigation.