In this study, earthquake rupture models for future mega-thrust earthquakes in the Nankai–Tonankai subduction zone are developed by incorporating the main characteristics of inverted source models of the 2011 Tohoku earthquake. These scenario ruptures also account for key features of the national tsunami source model for the Nankai–Tonankai earthquake by the Central Disaster Management Council of the Japanese Government. The source models capture a wide range of realistic slip distributions and kinematic rupture processes, reflecting the current best understanding of what may happen due to a future mega-earthquake in the Nankai–Tonankai Trough, and therefore are useful for conducting probabilistic tsunami hazard and risk analysis. A large suite of scenario rupture models is then used to investigate the variability of tsunami effects in coastal areas, such as offshore tsunami wave heights and onshore inundation depths, due to realistic variations in source characteristics. Such investigations are particularly valuable for tsunami hazard mapping and evacuation planning in municipalities along the Nankai–Tonankai coast.