Climate change can change the environmental conditions, influence the species distribution, and even threaten the viability of some species. In this paper, we simulate and predict the geographical distribution and their main environmental factors of Amygdalus mongolica in the past (1970-2000) and future (2081-2100) climate conditions by using ArcGIS software and MaxEnt (Maximum entropy) model. The results showed that:(1) under the past climatic conditions, Amygdalus mongolica had good suitability in the southeast of Qilian Mountains. (2) The suitable areas of Amygdalus mongolic under four climate change scenarios (SSP126, SSP245, SSP245, SSP585) had the risk of disappearance in the south and southeast of Qilian Mountains, and the expansion areas were concentrated near the national park in the north-central Qilian Mountains. (3) The distribution pattern of Amygdalus mongolica would migrate to the northern and high altitude areas in Qilian Mountains; (4) The contribution of the wettest monthly precipitation (Bio13), slope (Slope), the coldest seasonal average temperature (Bio11), and the maximum temperature of hottest month (Bio5) reached more than 80%, which were the main factors affecting the distribution of Amygdalus mongolica. The study simulated, analyzed and predicted the potential distribution changes of Amygdalus mongolica in Qilian Mountains under past and future scenarios, providing scientific basis for the protection of ecology and biodiversity in Qilian Mountains.