We studied the seismic structural response of a model of fault‐structure system with fine resolution using multiscale analysis with parallel simulation of seismic‐wave propagation. Our goal was to generate a numerical model with less geometric approximation for use in fault‐structure system analysis that includes the crust, soil, and building structure. In the multiscale analysis, the solution of the fault‐structure system was estimated using a two‐step process. First, the solution of a low‐resolution model (at a geologic‐length scale) was computed. Then, this solution was used as an input boundary condition to the high‐resolution model (at an engineering‐length scale). The final solution from this process is thought to be an acceptable estimate of a direct analysis of a fault‐structure system. To reduce the computation time of the simulation from fault to ground surface (at a geologic‐length scale), we implemented parallel simulation of seismic‐wave propagation based on domain decomposition by a prepartitioning method. This method is based on automated multiresolution (hybrid grid) meshing of subdomains in a distributed‐memory computer. We also performed verification and validation tests with application to maximum target frequency of 1.0 Hz. Finally, we computed the dynamic responses of a fault‐structure system model that included a nuclear power plant as the building structure using a fine‐resolution model based on realistic conditions.