Detailed three-dimensional images of P and S wave velocity and Poisson’s ratio (σ) of the crust and upper mantle beneath Kyushu in SW Japan are determined, with a focus on the source area of the 2016 Kumamoto earthquake (M 7.3) that occurred in the Beppu-Shimabara graben (BSG) where four active volcanoes and many active faults exist. The 2016 Kumamoto earthquake took place in a high-velocity and low-σ zone in the upper crust, which is surrounded and underlain by low-velocity and high-σ anomalies in the upper mantle. This result suggests that, in and around the source zone of the 2016 Kumamoto earthquake, strong structural heterogeneities relating to active volcanoes and magmatic fluids exist, which may affect the seismogenesis. Along the BSG, low-velocity and high-σ anomalies do not exist everywhere in the upper mantle but mainly beneath the active volcanoes, suggesting that hot mantle upwelling is not the only cause of the graben. The BSG was most likely formed by joint effects of northward extension of the Okinawa Trough, westward extension of the Median Tectonic Line, and hot upwelling flow in the mantle wedge beneath the active volcanoes.