Abstract: To take into account the frequency dependency of foundation impedance and avoid repeated Fourier transform, a time-domain difference approach for calculating the ground resisting forces was introduced by the authors. The software programs of structure history analysis were re-developed based on general FEM software, and the dynamic history analysis module of considering the soil-structure interaction effect was included. Finally, multilayer frame with circular foundation on the surface of layered soil media is numerically analyzed under three dimensions earthquake excitation. Numerical results demonstrate that the proposed approach can reflect the property of foundation impedance which varies with frequency in soil-structure system.