Abstract: In the analysis of structural seismic response considering the influence of local site, reasonable and effective seismic input is crucial. Based on the domain reduction theory, a two-step simulation method coupling the spectral element method (SEM) and the finite element method (FEM) is developed in this study. Firstly, SEM combined with MTF is used to simulate the displacement response of the model with structures being removed under plane wave incidence, and the responses of the boundary zone nodes defining the localized soil-structure calculation domain is directly used as the input for the soil-structure region. Secondly, the FEM is used to simulate the dynamic response of the soil-structure system, and the scattered waves caused by the structure is absorbed by the MTF. Compared with traditional DRM method, this method avoids the calculation of equivalent node forces at artificial boundaries, and the same calculation scheme can be used for different attribute medium. The accuracy and effectiveness of the proposed method were verified based on the uniform half space model, the basin model and the local canyon model. Finally, by comparing the seismic responses of a subway station and a frame structure with and without considering the basin effect, the importance of considering local site effects in simulating structural seismic response was verified.