Shrubs were the most important dominant plants in desert areas of China. Sand binding shrubs not only are vital to stabilize sand dunes in the desert, but also are beneficial to improve ecological restoration in the desert ecosystem. Based on a long-term monitoring and study( > 50 years) at the Shapotou Desert Research and Experimental Station,which is located on the southeast edge of the Tengger Desert, we simulated the processes of the cover of sand-binding shrub and deep soil water content using an eco-hydrological model. The model revealed that the establishment of sand-binding shrub resulted in change in the hydrological processes comparing to the mobile sand dunes. The cover of sand-binding shrub and deep soil water content had reached to a new equilibrium after 50 years the sand-binding shrub established. The balance was the cover of sand-binding shrub remained stable at (10±0.9)% and the deep soil water content remained stable at (2.58±0.2)%. In the Shapotou area of the Tengger Desert, the coverage of shrubs and biological soil crust were about 10% and 60% respectively, and the deep soil water content maintained at 3%, reflecting the maximum soil water carrying capacity of the vegetation.