Although drilled samples of fault rocks have yielded information on frictional features of shallow subduction zones, the relationship of rupture propagation to the levels of friction and pore-fluid pressure remains uncertain. To investigate this topic, we performed dynamic rupture simulations along the megasplay fault that slipped during the 1944 Mw 8.0 Tonankai earthquake in the Nankai Trough. We used actual data from friction experiments on rocks from the fault segment and pre-existing pore pressures deduced from geophysical surveys for the shallow portion of 0–10 km depth along the fault. Simulations of low friction (friction coefficient ca. 0.04) produced large slip (about 30 m), whereas simulations using higher friction (friction coefficient ca. 0.2) suppressed the rupture. In simulations with low friction in which the pore-fluid pressure was nearly equal to the lithostatic stress, the slip decreased to about 25 m. However, when the simulations included slip-strengthening at shallow depth and higher friction, the slip still reached roughly 20 m. Such variability in slip during rupture propagation is caused by differences in the friction features and fluid pressure conditions of fault rocks, in which the friction features might be related to the mineral composition. Spatiotemporal heterogeneity in fault-rock type and their physical and hydraulic properties may fundamentally produce the complexity and variability of earthquake rupture propagation along the Nankai plate-subduction boundary.