The 3D wave propagation simulation is suitable for the long‐period ground‐motion hazard analysis, because the realistic seismic source and velocity structure models are applicable and ground motion at any point can be obtained. However, large‐scale simulations for various scenarios are needed to adopt uncertainty due to the source model of a large earthquake. Here we show our approach to overcome a problem of heavy computational expense. We improve computation performance of the 3D finite‐difference method by using discontinuous grids and by adapting to multigraphics processing units technique. Then, we simulate long‐period ground motion of many scenarios of a hypothetical megathrust earthquake in the Nankai trough. We use the characterized source models based on the “recipe” in the simulation. Finally, we apply the simulation results based on about 400 scenarios to a technical framework of the probabilistic seismic‐hazard analysis. The hazard maps of velocity response spectra for a given conditional exceedance probability show that the long‐period ground motion is more significant with respect to the underground structure than is the distance from the source area.