Abstract: To improve the computational efficiency of a 3D nonlinear dynamic problem of a soil-structure interactive system, based on the characteristic that structures have local plastic regions, the mixed linear-nonlinear constrained mode synthesis method, suitable for nonlinear substructure coupled with several linear substructures at the interface boundaries, is presented. This method divides the system into linear and nonlinear substructures. The dynamic response of the whole nonlinear system can be obtained by reducing the degree of freedom of linear substructures using mode cut-off criterion based on potential energy criterion and synthesizing with the nonlinear substructure. Furthermore, the proposed method is used to solve the 3D soil and multi-story buildings interaction system dynamic problem and several dynamic analyses has been carried out according to two kinds of soil boundary conditions by different seismic excitations. The analysis results indicate that the proposed method is accurate and effective. Finally, the nonlinear soil region scale is studied by several groups of numerical experiments, the comparison results show that the satisfactory result can be obtained when the range of nonlinear substructure gets 3 times of superstructure's, the effectiveness of the proposed method has been further verified.