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The location of the Integrated Ocean Drilling Program’s (IODP) Nankai Trough Seismogenic Zone Experiment (NanTroSEIZE) was based on regional two-dimensional seismic reflection surveys carried out by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). Final site locations were chosen based on a three-dimensional (3-D) seismic reflection survey acquired across the seaward margin of Kumano Basin and the accretionary prism from the basin to the deformation front. This survey covered a region 12 km wide (approximately parallel to the regional structural strike) and 56 km long (approximately perpendicular to the regional strike) and provided detailed images of the structure and seismic stratigraphy of the drill sites. Sites were drilled in the frontal thrust zone at the toe of the accretionary prism, the frontal region of the megasplay fault zone, and the forearc basin. The 3-D seismic data volume images a main frontal thrust at the prism toe with the hanging wall thrust at least 7.5 km seaward over the trench. This configuration is different from that in other parts of the Nankai prism. At the shallow end of the megasplay, the data images a complex thrust system that truncates older structures in the underlying accretionary prism and shows that the hanging wall block has overridden more than 1250 m of young slope sediments. At the forearc basin site, we interpret landward-dipping forearc basin strata onlapping older slope sediments, which in turn overlie an older part of the accretionary prism.