This paper proposes a nonlinear time‐domain finite‐element method to generate three‐direction seismic loads on the mesh boundary using the measured ground surface acceleration. The proposed scheme obtains correct earthquake responses around the major soil‐structure interaction (SSI) region. The applied acceleration at the mesh bottom is first approximated as the measured acceleration on the soil surface. A time‐domain finite‐element analysis and a deconvolution scheme are then performed to find the seismic acceleration at the mesh bottom. After several iterations, these acceleration data can be convergent to an acceptable accuracy. This paper also investigates the viscous and absorbing boundary methods to avoid fake reflection along the mesh boundary. The viscous boundary method is simple and can be applied to a standard finite‐element code without difficulty; moreover, this scheme is also acceptably accurate, if appropriate damping is used in the interface layer. Thus, the viscous boundary method is suggested for use in the SSI analysis with the earthquake loading.