The effective simulation of soil-structure interaction and the nonlinear characteristics of soil is a key technical problem for conducting a seismic response analysis of soil foundations on nuclear island. A one-dimensional finite element model of nuclear structure is established on the software platform of SuperFLUSH by simulating the radial damping through setting viscous artificial boundary in the limited area of foundation to analyze the response of free field to the ground motion input, then to describe the nonlinear dynamic characteristics in the near field ground using equivalent linear method. Furthermore a case study of a simplified lumped mass model for CPR1000 nuclear reactor in the soil foundation is investigated about the effect of SSI and nonlinear layered soil foundation on the seismic response characteristics of nuclear island building structure. Numerical results verify the reliability and applicability of the proposed model in engineering application. With the consideration of SSI effect, the model of viscous artificial boundary can effectively absorb the energy of scattered waves and reduce structural response. With the consideration of the nonlinear characteristics of soil, the acceleration amplitudes decrease to a certain extent in different directions, and the peak frequency shifts to low frequency. Based on above analysis, the combination of SSI and the nonlinear characteristics of soil is necessary for seismic analysis of nuclear island.