More than 13,000 arrival times of 562 local shallow earthquakes selected from the Japan University Network Earthquake Catalog are used to investigate the seismic velocity structure of the crust beneath the Japan Islands. We simultaneously determined the hypocenter parameters, P- and S-wave station corrections and depth distributions of the Conrad and Moho discontinuities beneath the whole of the Japan Islands by applying an inversion method. The P- and S-wave station corrections show similar distribution patterns. They are negative (relatively late arrivals of seismic waves) in Hokkaido and positive (relatively early arrivals of seismic waves) in western Japan. In eastern Honshu, they are positive along the coast of the Pacific Ocean and negative in the land area and along the coast of the Japan Sea. The Conrad discontinuity is located at a depth range from 12 to 22 km. In Hokkaido, the Conrad is shallow in the eastern pan and becomes deep toward the west. In NE Honshu the Conrad is deep beneath the land area, and becomes shallow toward the surrounding seas. In western Japan, the Conrad is shallow in the northern part and becomes deep toward the south. The Moho is located in a depth range from 25 to 40 km. In Hokkaido, the Moho has the shape of a circular cone with a maximum depth of 36 km. In most parts of the Japan Islands, the Moho is deep beneath the land area and becomes shallow toward the surrounding seas. The Moho is deepest, up to 40 km, beneath the central part of the Chubu District.