The stone pagoda of Mireuk temple site is currently restoring through the repairing process. This stone pagoda has the various construction types in the inner and outer space. Therefore, the stress concentration and structural behavior need to be considered through the analysis of various construction patterns. To this end, this study presents the structural modelling and analysis considering the discrete element analysis technique to solve the discontinuum behavior between the stone elements. Also, this study performs the structural performance evaluation through the various design variables for the safety of stone pagoda. Through the analysis results, we can find out the small stress concentration in the several members. But, because the stresses and displacements are relatively small, we can secure the safety of the whole structure.