This article aims at numerically simulating the 3D seismic wave propagation from rupture to structures. A two‐step method coupling the spectral element method (SEM) and the finite‐element method (FEM) is proposed based on the domain reduction method to simultaneously simulate the seismic wave propagation in large‐scale regions and analyze the dynamic behavior of structures in local sites. First, the concept of the proposed two‐step method is illustrated. In the first step, the seismic wave propagation of the entire area, involving the source, propagation media, and local region of interest, is simulated using the SEM. In the second step, the dynamic analysis of structure‐foundation system with local geological and topographical conditions is implemented using the FEM in a fine mesh based on the results in the first step. Subsequently, the FEM grid size is evaluated to match the SEM results, and the proposed SEM–FEM procedure is verified using both point‐source and finite‐fault model in a layered flat model. Finally, two analysis examples are presented using the proposed procedure. The analysis results show that the proposed SEM–FEM procedure can well consider the effects of local geological and topographical conditions on synthesized ground motions and can be applied to the rupture‐to‐structure simulations in earthquake engineering.