One of the more prominent architectural elements of the Nankai subduction margin, offshore southwest Japan, is an out‐of‐sequence thrust fault (megasplay) that separates the inner accretionary prism from the outer prism. The inner prism (hanging wall of the megasplay) is dominated by mudstone, which is enigmatic when the sedimentary facies is compared to coeval deposits in the Shikoku Basin (i.e. inputs from the subducting Philippine Sea plate) and to coarser‐grained turbidite sequences from the Quaternary trench wedge. Clay mineral assemblages amplify the mismatches of sedimentary facies. Mudstones from the inner prism are uniformly depleted in smectite, with average bulk values of 23–24 wt%, whereas the Shikoku Basin deposits show progressive decreases in proportions of smectite over time, from averages of 46–48 wt% at 10 Ma to 17–21 wt% at 1 Ma. Plate‐boundary reconstructions for the Philippine Sea region provide one solution to the conundrum. Between 15 Ma and 10 Ma, the Pacific plate subducted near the NanTroSEIZE transect, and a trench‐trench‐trench triple junction migrated to the northeast. Accretion during that period involved sediments that had been deposited on the Pacific plate. Motion of the Philippine Sea plate changed from 10 Ma to 6 Ma, resulting in sinistral slip along the proto‐Nankai Trough. Sediments accreted during that period probably had been deposited near the triple junction, with a hybrid detrital provenance. Renewed subduction of the Philippine Sea plate at 6 Ma led to reorganization of watersheds near the Izu–Honshu collision zone and gradual incision of large submarine canyons on both sides of the colliding Izu arc. Accreted Pliocene mudstones share more of an affinity to the triple junction paleoenvironment than they do to Shikoku Basin. These differences between subducting Shikoku Basin strata and accreted Pacific plate sediments have important implications for interpretations of frictional properties, structural architecture, and diagenetic fluid production.