Rock materials of the three-storied stone pagoda in the Cheongryongsa temple in Korea are mainly composed of gneissose two-mica granite and fine-grained granite. This stone pagoda shows structural instability due to cracks and breaking-out of the stones. The surface properties of the stone is highly degraded by various inorganic pollutants and epilithic biospecies. Therefore, this study carried out comprehensive deterioration diagnosis by non-destructive methods, and some conservation treatments base on the diagnosis were carried out to reduce weathering progress. As the treatments, the biospecies and lichen that covering on the stone surfaces were removed by dry and wet cleaning, and degraded concrete applied to the pagoda for restoration in the past was removed and repaired with epoxy resin. Oxidized iron plates inserted between the rock properties were also substituted titanium stainless steels. After all processes are completed, we sprayed consolidant on the rock surface. Finally, the ground of the stone pagoda was rearranged using small rock aggregates, and the fence was established for control of artificial deterioration by visitors and environmental maintenance.