Generally, stone pagoda structures have been constructed by stacking the masonry stone members. The problem about the safety and stability of masonry stone structure is due to the structural behavior of discontinuum surface between the contact stones rather than the failure by the lack of material strength. The masonry stone structure has the big difference with the analysis method of continuum structure as discontinuum structure. Therefore, the masonry stone should be treated as discontinuum structure that can express mechanical behavior of discontinuum surface between the contact stones. The friction between contact stones of discontinuum structure is a very important factor that affects the behavior of discontinuum surface. Especially, the roughness of discontinuum surface affects the friction. Therefore, we carry out the direct shear test of discontinuum surface for the evaluation of structural behavior according to roughness of the discontinuum surface of stone pagoda and study the characteristics of discontinuum surface according to various roughness. Also, we apply the characteristics of discontinuum surface to stone pagoda model. Finally, we estimate the structural behavior of stone pagoda according to the friction of discontinuum surface.