The Mikawa Bay Region, central Japan, is characterized by many active faults recording Quaternary activities. It is, however, difficult to understand the overall tectonic character of the region due to a thick sedimentary cover. We report the first finding of Neogene basin inversion in southwest Japan by estimating the depth and structure of the basement surface in the Mikawa Bay Region by analyzing gravity data. Our gravity basement map and two-dimensional density-structure modeling revealed a half graben bounded on the south by the north-dipping Utsumi Fault. The motion of the Utsumi Fault, which inverted from normal faulting during the Miocene to recent reverse faulting, indicated the inversion of the half graben. The timing of the inversion of the fault motion, i.e. the reverse faulting of the Miocene normal fault, can be compared with an episode of basin inversion observed at the eastern margin of the Japan Sea, northeastern Japan. The Takahama Fault in the southwestern part of the Nishi–Mikawa Plain is considered to have formed as a result of the backthrust of the Utsumi Fault under inversion tectonics. If the Takahama Fault is indeed the backthrust fault of the Utsumi Fault, the root of the Takahama Fault may be deep such that the Takahama Fault is seismogenic and linked to the 1945 Mikawa earthquake.