It is inevitable to use the distinct element method in the analysis of structural dynamics for stacked stone pagoda system. However, the experimental verification of analytical results produced by the discrete element method is not sufficient yet, and the theory of distinct element method is not universal in Korea. This study introduces how to model the stacked stone pagoda system using the distinct element method, and draws some considerations in the seismic analysis procedures. First, the rocking mode and sliding mode are locally mixed in the seismic responses. Second, the vertical stiffness and the horizontal stiffness on the friction surface have the greatest influence on the seismic behavior. Third, the complete seismic analysis of stacked stone pagoda system requires a set of the horizontal, vertical, and rotational velocity time histories of the ground. However, earthquake data monitored in Korea are limited to acceleration and velocity signals in some areas.