This study focus on the suggestion of standard legend, the process system on making method of deterioration map, the development of crack index (CI), and the evaluation techniques of surface and 3D deterioration rate for stone cultural heritage. The standard legends of deterioration forms were made using a common graphic program after crack, blistering, scaling, break-out, granular disintegration, and perforation were subdivided. The deterioration map improved accuracy and reliability on deterioration range using 3D digital restoration and high resolution photograph mapping technique. Also, quantitative deterioration evaluation of stone cultural heritage was carried out developing the crack index, and the 3D deterioration rate of a break-out part was calculated by virtual restoration modeling. As a quantitative deterioration evaluation of Magoksa Temple stone pagoda based on the results described above, the north face showed high deterioration rate of bursting crack (1.70), hair crack (1.34), scaling (20.2%) and break out (13.0%), and the 3D deterioration rate of first roof stone was 6.7%.