Abstract: A model is proposed for nonlinear seismic response of 3D canyon in deep soft soils. In the model, the viscous-elastic boundary and the equivalent node force input method are combined for wave motion input, and the equivalent linear method is introduced for nonlinear soil behavior. The model is based on the general finite element software ABAQUS. The accuracy of the model is verified by comparing with the results in the existing literatures. Nonlinear seismic response of a 3D shallow canyon in deep soft soils is performed and compared with the linear response, and the influence of canyon on nonlinear seismic response is analyzed. Finally, the nonlinear response of the 3D shallow canyon under excitation of the artificial wave from seismic safety evaluation is presented. It is shown that the nonlinear behavior of soils has significant effect on the seismic response of the 3D canyon. The nonlinear seismic response can be greater than the linear response near the canyon center, as a result of wave scattering by the 3D canyon, and it is more obvious for a larger seismic excitation. The proposed model is valuable for analyzing the nonlinear seismic effect of complex local sites.