Two research cruises that deployed submersible surveys were undertaken along the Tenryu Submarine Canyon to directly observe the structural architecture of the eastern Nankai Accretionary Prism off the coast of southern Japan. The surveys have demonstrated that the accreted sediments are strongly deformed turbidite sequences that occur in repeated thrust-anticline structures. From the leading edge of the prism near the trench toward the arc, the following deformation zones have been identified within the prism: Frontal Thrust zone, Prism Toe zone, Imbricate Thrust zone, and Tokai Thrust zone (or out-of-sequence thrust or OOST zone). The Frontal Thrust zone is characterized by debris deposits within the hanging wall that have an age of 0–0.43 Ma, as determined from radiolarian biostratigraphy. The Prism Toe zone is characterized by unconsolidated turbidite sequences that are 1.98–3.4 Ma; these sequences are cut by normal and thrust faults. The Imbricate Thrust zone includes consolidated muddy layers and unconsolidated sandy layers that contain numerous fracture cleavages. The OOST zone consists of highly deformed consolidated sediments, ranging in age from 0.18 to 1.03 Ma. From the Prism Toe zone to the Imbricate Thrust zone, the uniaxial compressive strength increases gradually from 0.5–3.0 to 1.0–6.0 MPa, while the anisotropy of magnetic susceptibility changes from oblate to prolate shapes, and porosity decreases from 40%–50% to 30%–50%. These data indicate that the eastern Nankai Accretionary Prism appears to have been deformed toward the Imbricate Thrust zone just south of the OOST. Stable isotope analyses of calcite veins and calcite cement of the sandstone samples from the Tokai Thrust zone have shown that fluid temperatures for calcite precipitation were 24–63 °C in the OOST zone. The occurrence of highly deformed and consolidated rocks within the Nankai Accretionary Prism likely resulted from tectonic transportation of deeply buried rocks along major out-of-sequence thrust faults, such as the Tokai OOST. We infer therefore that out-of-sequence thrust faults play a major role in transporting deeply buried, deformed rocks in accretionary prisms to the shallower depths and even to the seafloor during ongoing subduction.