The N tip of the Izu-Ogasawara Arc on the Philippine Sea plate collided with the central part of the Honshu Arc in the early Quaternary. The collision history is recorded in late Cenozoic strata that are distributed widely in central Japan. To reconstruct paleotopography during the collision process, paleogeographic maps of central Japan were drawn at six time slices during the late Cenozoic. The paleodepth of the area between the Izu-Ogasawara Arc and the Honshu Arc changed quickly from deep-sea to shallow marine during the Quaternary by means of rapid deposition of large amounts of coarse-grained detritus. The conglomerate was first deposited in a trough as deep-sea fan deposits, and filled the trough until an alluvial fan was formed. Forearc basins of the Honshu Arc facing the collision area subsided from 3 to 1 Ma. The tectonic inversion seen in sedimentary basins in the Kanto and Tokai regions might be closely related to the change of motion of the Philippine Sea plate. However, a basin of the Ashigara area sunk continuously without interruption until 0.7 Ma. The collision event affected strongly distribution of deep-sea benthic foraminifera. Paleogeographic maps show that a deep trough appeared in the Ashigara area between 3 and 1.5 Ma. This trough may have served as a passage for the migration of deep-sea benthic foraminifera between the Pacific and the Philippine Sea.