Abstract: In the analysis of structural seismic response considering the influence of local site conditions, 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, the method of SEM combined with MTF is used to simulate the displacement response of the model that encompasses the localized feature from which the structure has been removed under plane wave incidence, and the displacement responses of the boundary zone nodes defining the localized soil-structure calculation domain are directly used as the input for the truncated soil-structure region. In this step, a relative coarse mesh that just meet the requirement of the highest resolved frequency of the background model can be adopted by the merits of SEM. Secondly, based on the above input wave filed that has incorporated the effect of the local heterogeneity, the FEM is used to simulate the dynamic response of the soil-structure system, and the scattered waves caused by the structure are absorbed by the MTF, in which a quite finer mesh can be used for the structure domain. Compared with traditional DRM method, this method avoids the calculation of equivalent nodal forces at artificial boundaries required for the seismic motion input, and the same calculation scheme can be used for medium with different attributes. The accuracy and effectiveness of the proposed method were verified based on the comparison of solution using direct method for the uniform half space model, the basin model and the local canyon model, and the influence of the selected sub-region shape as well as the order of MTF on the simulated results is discussed. Finally, by comparing the seismic responses of a subway station model and a frame structure model with and without considering the basin effect, the importance of considering local site effects in simulating structural seismic response was verified.