Three-dimensional seismic velocity structure in and around the Philippine Sea plate subducting beneath southwestern (SW) Japan is determined by applying double-difference tomography method to arrival time data for earthquakes obtained by a dense nationwide seismic network in Japan. A region of low S wave velocity and high Vp/Vs of several kilometers in thickness is recognized immediately above the region of intraslab seismicity in a wide area from Tokai to Kyushu. This characteristic layer dips shallowly in the direction of slab subduction. Compared with the upper surface of the Philippine Sea slab based on seismic reflection and refraction surveys on seven survey lines, we interpret that the low-Vs and high-Vp/Vs layer corresponds to the oceanic crust of the Philippine Sea slab. On the basis of the position of the low-Vs and high-Vp/Vs layer and the precisely relocated hypocenter distribution of intraslab earthquakes, the upper surface of the Philippine Sea slab is reliably determined for the entire area of SW Japan. Nonvolcanic deep low-frequency earthquakes that occurred associated with the subduction of the Philippine Sea slab are distributed along the isodepth contour of 30 km in SW Japan, except for the Tokai district where the depth of deep low-frequency earthquakes becomes gradually deeper toward northeast.