Abstract: In order to study the influences of nonlinear response of low-wave velocity soil on near-fault ground motion in three-dimensional sedimentary basin, and realize the simulation of three-dimensional complex site ground motion based on the whole process of physics (source rupture-seismic wave propagation-complex site effect-near-surface soil nonlinear response), the secondary development is carried out in the spectral element method code-SPECFEM3D. The three-parameter Martin-Seed-Davidenkov constitutive model with generous engineering applications and suitable for different soil types is adopted. Based on the existing irregular loading and unloading criteria, the real-time updating of shear modulus of soil and the effective identification of loading and unloading inflection points are realized by modifying the stress increment at each explicit time step in the code. The nonlinear characteristics of soil are incorporated into the three-dimensional complex site ground motion simulation. The established three-dimensional model is first degenerated to one-dimensional one by applying a reasonable boundary, and compared with the results of one-dimensional nonlinear dynamic analysis software DEEPSOIL to verify the correctness of the development. Furthermore, the developed code is applied to the nonlinear ground motion simulation of the Shidian Basin in southwestern Yunnan province, China, and compared with the corresponding linear results. The results show that the peak values of acceleration and velocity in Shidian area are lower than those of linear results, and the influences of nonlinear soil on PGV are more obvious, which is about 30% lower than that of linear results. The deposition nonlinearity reduces the velocity and amplitude of response spectra of the receivers inside the deposition, and the characteristic frequency moves to the long period direction.