Based on the principle of the dynamic substructure method, the mixed linear-nonlinear constraint modal method was proposed and applied to analysis of the two-dimensional nonlinear dynamic problem caused by the interactions between the foundation soil, box-type foundation, and upside shear wall structure under complex conditions. The complex conditions included the uniform viscoelastic boundary problem and the highly nonlinear contact problem between the foundation and surrounding soil. According to the local nonlinear feature of the soil-structure interactive system, the system was divided into several linear and nonlinear substructures. During the dynamic time history analysis, the self-compiled program based on second development was used to extract the equivalent characteristic matrices gradually for all the nonlinear substructures, which were combined with the linear substructures reduced by potential energy criterion-based truncation criterion. Then, synthesized modal processing was performed, and substructure equations considering the contact problem and involving the uniform viscoelastic boundary were deduced. Thus, a synthesized modal equation for each substructure was formed under the complex conditions. Results show that the dynamic response time history curves of the displacement, velocity, acceleration, horizontal shear force, bending moment, and interlayer displacement angle obtained by the mixed constraint modal method agree with those obtained by the ANSYS method, demonstrating that the mixed linear-nonlinear constraint modal method is an effective and feasible method of solving the soil-structure dynamic interaction problem under the complex conditions.