Analysis of dynamic behavior of soil-structure interaction (SSI) is a complicated problem due to the complexities of soil behaviors and dynamic analysis. It is difficult to solve SSI with analytical methods. However, numerical methods with highly developed computer technique are efficient. Based on the advanced nonlinear finite element analysis software MSC.Marc, SSI on loess ground is studied. An approach for the application of MSC.Marc in SSI analysis is presented and an example is given. Hyperbolic soil constitutive relationship and viscous boundary conditions are adopted in the soil model. Moreover, contact between the embedded columns and the adjacent soil is considered. Response spectrum analysis of the result is carried out. Some conclusions about the seismic response of soil-structure system under different soil stiffness and different soil-layer thickness conditions are given. A new way of analyzing SSI for loess ground is provided.