Understanding the factors controlling earthquake rupture areas in subduction zones is a fundamental question in geodynamic research. In the Nankai Trough, Japan, three major controlling factors have been proposed so far: surface roughness, such as seamounts, on the subducting Philippine Sea plate, a locally dense and rigid upper plate, and stable or unstable frictional properties of the plate-boundary megathrust with abnormal pore-fluid pressure. The most prominent rupture segment boundary in the Nankai Trough is located off the Kii Peninsula. When the rupture starts and propagates beyond this boundary, the entire megathrust breaks, as in the 1707 Hoei earthquake. When the rupture does not propagate beyond this portion, the rupture area is segmented, as in the 1854 Ansei, 1944 Tonankai, and 1946 Nankai earthquakes. In this case, the boundary works as a barrier. The asperity or barrier depends on the frictional behavior along the megathrust in this area. Thick and dense plutonic rocks are the main component of the upper plate of the Kii Peninsula. Magmatic activity associated with the proto–Izu-Bonin arc collision is speculated to have occurred in the middle Miocene. Thus, we propose that the long-term tectonic hysteresis of the upper plate is the main factor controlling the rupture area segmentation in the Nankai Trough.