The velocity structure and accurate aftershock distributions of the 2004 mid-Niigata prefecture earthquake are elucidated by inverting the arrival times from 716 aftershocks using double-difference tomography. Fourteen temporal seismic stations were immediately deployed in and around the source region within 46 h of the occurrence of mainshock. The seismic velocities in a hanging wall are lower than those in a footwall, and the velocity contrast extends to a depth of approximately 10 km. The aftershocks associated with the mainshock are distributed around the clear boundary between the low and high velocity structures. It is interpreted that the mainshock fault plane of the mid-Niigata prefecture earthquake was reactivated as a reverse fault since the crustal shortening initiated at 3.5 Ma. Crustal stretching or shortening along the Japan coastline has created complex structures such as low velocity zones, which can potentially control the seismic activities around the source region.