Sedimentary basins can have significant amplification effects on seismic ground motion. It is very necessary to use appropriate nonlinear soil constitutive model to quantitatively analyze the seismic response of three-dimensional (3D) sedimentary basins subjected to strong ground motion. This paper employs a bounding surface constitutive model to simulate the soil nonlinearity, which is successfully incorporated into ABAQUS software. A finite element model is then established to investigate the nonlinear seismic response of 3D sedimentary employing the constitutive model along with viscoelastic artificial boundary and equivalent nodal force method. The nonlinear amplification effect of a typical 3D layered sedimentary basin is extensively evaluated. The influence of a soft interlayer in the sedimentary basin on the seismic amplification is further analyzed. The results demonstrate that the maximum surface peak acceleration usually occurs in specific areas; as the input ground motion intensity increases, the focusing and amplification effects become more significant in deeper soil layers. A soft interlayer will significantly increase the short period component of the surface response spectrum, and shorten the predominant period of sedimentary basin. These results can provide a reference basis for seismic risk analysis and determination of ground motion parameters in a sedimentary basin.