The threedimensional vertical column system and the multiyield surface plasticity constitutive model were implemented for the problem of nonlinear seismic site response to bidirectional horizontal earthquake loading. The practical issue concerned the specification of the accuracy and efficiency of site response analysis. The crucial parameters describing the multiyield surfaces, soil thickness division and boundary conditions, and frequencies or modes for the damping formulation could help preforming the accurate nonlinear seismic ground response in the bidirectional earthquake. The layered soil column was divided into multiple subsoils with different viscous damping matrixes according to the shear velocities as the soil properties were significantly different. The accuracy of the threedimensional soil column method was verified by the dynamic centrifuge model test results. It is concluded that the threedimensional vertical column model can be used for bidirectional nonlinear seismic local ground response analysis.