AbstractWe present a three‐dimensional P and S wave tomography model beneath the central Japan Sea using arrival time data obtained by long‐term ocean bottom seismometer observations. The tomographic model is determined down to over 300 km. The resulting tomographic image has two features in the mantle wedge. First, a remarkable low‐velocity region is spread within the shallow part of the mantle wedge beneath the Japan arc with a slight extension beneath the Japan Sea. Second, an inclined low‐velocity anomaly exists in the deeper part beneath the Japan Sea and converges to the slab at ~300 km depth. Moreover, its anomaly amplitude is distinctly small compared to the shallow part of the low‐velocity region. These low‐velocity anomalies are interpreted to represent fluids that were dehydrated from the Pacific and Philippine Sea slabs and melt production affected by the fluid. Our observations suggest that the deep dehydration from the Pacific slab is found at a depth of approximately 300 km and large‐scale upwelling flow mechanically induced by plate subduction exists beneath the Japan Sea. Our results indicate the importance of the deep heterogeneous mantle wedge structure beneath the Japan Sea with regards to better understanding the magmatism of the subduction dynamics in Japan and the evolution of the opening of the Japan Sea.