The stone pagoda continued to be damaged by weathering and corrosion over time, and natural disasters such as earthquake are accelerating the destruction of cultural properties. Stone pagoda has discontinuous structure behavior and is very vulnerable to the seismic load acting in lateral direction. It is necessary to analyze various design variables as the contact surface characteristics play an important role in the dynamic behavior of stone pagodas. For this purpose, contact surface characteristics of stone pagoda can be classified according to surface roughness and filler type, and representative model is selected and structural modeling and analysis are performed using the discrete element method. Also, the seismic load according to the repetition period is calculated and the dynamic analysis is performed considering the discontinuous characteristics of the stone pagoda. Finally, the seismic behavior characteristics can be analyzed by the evaluation of stresses, displacements and structural safety.