As we know, desert pavement is a superficial feature from wind erosion widespread throughout arid lands and plays a dynamic role in geomorphic, hydrologic, and ecologic processes. In these regions, the plant cover is low or inexistent. Desert pavement is usually covered with large, small, and angular stones. Spatial distribution of stones at the surface is reflecting rainfall distribution at the land surface. Our objective in this study was to determine the relationship between the surface physical characteristics of desert pavement (meter scale), water movement, subsoil, and plant cover. The density and type of cover in land surface are also investigated. For this purpose, two different areas (Hajaligholi playa, Damghan) with different geology were selected. In each region, profiles were dogged. In site one, six different profiles were dogged, and each profile samples in different horizons (0–10, 10–20, 20–30, 30–40, and 40–50 cm) were being taken. In site two, three profiles were dogged, and the same horizon samples were being taken. The type and density of vegetation were determined. Finally, two sites were being compared. The results showed that strong relationship is between the stone cover, soil genesis, and plant distribution. Physicochemical properties (particle sorting, stones rates, electrical conductivity, pH, and gypsum) highly depend on the upland geological characteristics of the region. Also, soil structure and salt concentration have strong relationship with stone component. The distribution and density of vegetation show strong linkage with these properties. Also, in sites with desert pavements and dense plant cover, soils are protected and, thus, reduce desertification (loss fertile soils).