There are a large number of rammed earthen sites in northwest China. For thousands of years, earthen sites have developed a series of deterioration types that include surface weathering, sapping, cracks, collapses, gullies, and so on. Surface weathering is a highly destructive type of soil deterioration which erodes the sites all the time. Flake peeling (flaking) is one of the main manifestations of weathering. In order to prevent flaking more scientifically and efficiently, it is necessary to quantitatively evaluate its development stage and degree. In this article, the Vajra Pagoda of Jiaohe Ruins was selected as the research area, and we explored how to use GIS to analyze the surface topography of 3D scanning data. Meanwhile, using the sequential minimum optimization (SMO) algorithm, the authors effectively identify the crust and original wall (wall outcroppings following the detachment of crust) in the evolution of flaking. Finally, the 3D roughness of the four facades was calculated. The calculations show that the roughness parameters D and R s can well characterize the development of flaking. In a period of flaking development, the change rule of D and R s first increases and then decreases. This study proves that it is feasible to quantify the development degree of flaking employing morphological characteristic parameters. Furthermore, the results of the study provide a basis for determining the degree of deterioration of the sites in future heritage management efforts, leading to more rational and efficient conservation.