In order to understand the generating mechanism of the western Tottori earthquake ( M 7.3) that occurred on 6 October 2000 in southwest Japan, we determined high-resolution 3D P- and S-wave velocity and Poisson’s ratio structures in the epicentral area. We used 17,542 P- and 13,831 S-wave high-quality arrival times from 721 Tottori aftershocks and other local microearthquakes recorded by the dense High-Sensitivity Seismic Network (Hi-net) installed recently on the Japan Islands. Significant variations of up to 4% for seismic velocity and 9% for Poisson’s ratio are revealed in the aftershock area. Areas with large coseismic slips and high aftershock activity are associated with high P-wave velocity ( V P ), high Poisson’s ratio and high electrical conductivity, which may represent strong and competent parts of the fault zone containing fluids. The western Tottori mainshock hypocenter is located in a boundary zone where both velocity and Poisson’s ratio change drastically. Both P- and S-wave velocities are slower in the lower crust under the mainshock hypocenter, and low-frequency microearthquakes were detected within the slow anomalies around the Moho discontinuity before and after the occurrence of the 2000 western Tottori earthquake. These results and other related evidence suggest that the strong crustal heterogeneity in the western Tottori source area is associated with fluids and arc magma under nearby the Daisen volcano, which may have influenced the nucleation and rupture process of the western Tottori earthquake. The arc magma and fluids are thought to result from the dehydration reactions of the subducting Philippine Sea slab in this region. These results suggest that the nucleation of shallow earthquakes could be controlled by a deep structure and regime and so it is important to study the deeper crust and upper mantle structure and processes for clarifying the generating mechanism of large crustal earthquakes.