Basing on the distribution data from field investigation, using GIS and ecological niche model (MAXENT) to simulate, analysis, and to reveal the potential distributions, patterns and determinant factors of Amygdalus mongolica in the Central Asian Desert. Buffer analysis, based on the appending of average occurrence probability of A.mongolica in different areas and the land use (principal highway, railway, and residents) data of our study area, was carried out for confirming the protection priority of different populations. Results show: (1)the potential distributions concentrated in Alax and East Gobi of Mongolia, in bayannur, Alxa Zuoqi, Ordos Plateau and western XiLin GuoLengmeng of Inner Mongolia, in central and eastern areas of Hexi Corridor, in northern Ningxia Hui Autonomous Region and Shaanxi province, and in the part areas of northern Heibei province; (2)the distribution-influencing factors of A.mongolica are mainly the extreme temperature and precipitation: the extremely low temperature and the most dought season precipitation;(3) the disturbance of human activities to suitable habitats of A. mongolica was evaluated quantitatively, and the obtained core and buffer areas of reserves, and can guide in situ conservation and protection priority of different populations of this species very well.