We present the three-dimensional structures of the P wave velocity (VP), S wave velocity (VS) as well as the P wave to S wave velocity ratio (VP/VS) beneath Mount Fuji and the South Fossa Magna, Japan, using arrival time data collected from 2002 to 2005 by a dense seismograph array. The high-resolution data set and improved methodology reveal not only several velocity features that are consistent with previous studies but also important new details that clarify the velocity structures associated with volcanic processes beneath Mount Fuji and the collision tectonics of the South Fossa Magna. One such particular feature is a low-VP, low-VS and low-VP/VS anomaly at depths of 7–17 km beneath Mount Fuji that corresponds with the locations of deep low-frequency (DLF) earthquakes. The coincidence of the velocity anomaly and the DLF locations suggests that supercritical volatile fluid, such as H2O and CO2, may be abundant in the low-VP/VS region and may play an important role in generating DLF earthquakes. This anomaly overlies a deeper low-VP, low-VS and high-VP/VS anomaly at depths of 15–25 km that may represent a zone of basaltic partial melt. A low-VP, low-VS and low-VP/VS anomaly is seen at depths of 6–14 km beneath Mount Hakone. Isovelocity surfaces (VP = 6.0 km/s and VS = 3.5 km/s) corresponding to the upper limit of hypocenter distribution below Mount Fuji may define the upper surface of the Philippine Sea plate whose existence in a seismic gap beneath Mount Fuji has been controversial.