A submarine channel system and basal ramps of a Quaternary mass-transport deposit (MTD) are shown to represent thrust fault activity in the Nankai accretionary wedge. Variations in channel bed slope, height and width of submarine channels and gullies indicate uplift and sediment bypass seaward from a margin-dominating out-of-sequence thrust, the megasplay fault (MSF), at < 1.67–1.46 Ma. Between ~ 1.05 and 0.85 Ma, a younger mass-transport deposit (MTD 6) was detached at different depths. Demonstrating the significant deformation observed in the study area, the direction of transport of MTD 6 differs 30°–45° from the strike of scarps and ramps at its base, which are parallel to the structural contours of thrust anticlines underneath. This character contrasts to the geometries frequently documented in frontally-emergent submarine landslides. Oblique basal ramps form significant boundaries between zones of MTD 6 with distinct acoustic and, suggestively, petrophysical properties. As a result of this study, we postulate that developed channel systems can erode the upper continental slope and lead to bypass of substantial volumes of sediment to distal parts of accretionary wedges. This process bears the potential of generating periods of more intense thrust-wedge deformation than those predicted by mathematical and physical models based on present-day taper geometries. On a regional scale, the observations in this paper are important as they indicate a more diffuse distribution of deformation in the Nankai accretionary wedge than previously assumed for the MSF region.