In this study, a coupled model based on the boundary element and the finite element methods is used to analyze the dynamic responses of two-dimensional model resting on layered soil medium under spatially varying ground motion effects. The dynamic response of the soil-structure systems is obtained in the frequency domain. The results of the finite element and the coupling finite-boundary element models are compared with each local soil conditions. In the seismic analysis of the system, the substructure method is employed. In the standard finite element model, both the structure and semi-infinitive soil medium are modeled by the finite elements, however, in the coupling finite-boundary element model, the structure and the soil medium are modeled respectively by the finite and boundary elements, both. In the last method, the special features and advantages of two methodologies are considered. In the coupling of finite-boundary element method, the equivalent finite element approach is used in which the boundary element region is transformed as an equivalent finite element and the final system is solved as a stiffness problem. Results of the study show that the coupling finite-boundary element method can provide realistic and effective modeling of soil-structure interaction problems as compared with standard finite element method results.