We utilized 188,766 P-wave and 179,328 S-wave high-quality arrival-time data from 14,666 local earthquakes to determine the three-dimensional (3D) seismic velocity (VP, VS), VP/VS ratio, crack density (ε), and bulk velocity (Vϕ) structures in and around the source areas of the 2004 and 2007 Niigata earthquakes (Japan Meteorological Agency magnitude [MJ] 6.8) in Japan in order to understand the generation mechanisms of the Niigata mainshocks. The aftershock hypocenters were relocated by applying the double-difference location method simultaneously with the tomographic inversion, indicating a complicated fault system that includes not only two parallel dominant faults dipping to the northeast but also some conjugate faults crossing the Niigata mainshock hypocenters. In general, high velocity (VP, VS) with low ε at 11 km depth is visible in the southeastern part of this area in contrast to anomalous low velocity with high crack density in the northwestern part along the Niigata-Kobe tectonic zone (NKTZ). These characteristics of the velocity and crack density are consistent with the spatial distribution of active faults along the NKTZ. The surface geological features that indurated pre-Neogene rock outcrops were observed in the southeastern area, whereas deep sedimentary basins were observed on the opposite side. Low VP and low VS zones with high VP/VS anomalies were imaged in and/or under the source areas, showing agreement with those revealed by previous studies. All the features of the velocity and VP/VS structures, together with the images of the crack density and bulk velocity, suggest the presence of fluids under the source areas. Such fluids might have weakened the mechanical strength of the fault zone of the source areas, thus triggering the 2004 and 2007 Niigata earthquakes. Our present study, together with other recent tomographic images, reveals that fluids penetrated into the source rocks from the lower crust and uppermost mantle as a result of dehydration of the subducting Pacific slab and thus may play a key role in the genesis of these large crustal earthquakes.