The South Fossa Magna region, central Japan, has been an active collision zone between the Honshu Arc and the Izu-Bonin Arc since the middle Miocene and provides an excellent setting for reconstructing the earliest stages of continent formation. Multi-system geo-thermochronometry was applied to different domains of the South Fossa Magna region, together with some previously published data, to reveal mountain formation processes, i.e., vertical crustal movements. Nine granitic samples yielded zircon U–Pb ages of 10.2–5.8 Ma (n = 2), apatite (U–Th)/He (AHe) ages of 42.8–2.6 Ma (n = 7), and apatite fission-track (AFT) ages of 44.1–3.0 Ma (n = 9). Thermal history inversion modeling based on the AHe and AFT data suggests rapid cooling events confined within the study region at ~6–2 Ma. The Kanto Mountains may have undergone a domal uplift in association with their collision with the Tanzawa Block at ~5 Ma. However, this uplift may have slowed down following the southward migration of the plate boundary and late Pliocene termination of the Tanzawa collision against Honshu Island. The Minobu Mountains and adjacent mountains may have been uplifted when motion of the Philippine Sea plate changed from northward to northwestward at ~3 Ma. Therefore, mountain formation in the South Fossa Magna region was mainly controlled by collisions of the Tanzawa and Izu Blocks and motional change of the Philippine Sea plate. Earlier collisions of the Kushigatayama Block at ~13 Ma and Misaka Block at ~10 Ma appear to have had little effect on mountain formation. Together with a clockwise rotation of the Kanto Mountains at 12–6 Ma, these observations suggest that horizontal deformation predominated during the earlier stage of arc-arc collision, and vertical movements due to buoyancy of the accreted crust resulting from crustal shortening and thickening developed at a later stage. •Low-temperature thermochronology in an active arc-arc collision zone•Rapid cooling/exhumation events coeval with collision event and plate motion change•Mountain formation controlled by collision events and plate motions