Restricted by factors such as regional climate and natural geographical location, the Altay Prefecture of Xinjiang has a very fragile ecological environment. As a strategic reserve area of non-ferrous metals in China, the mineral resources are very rich, while the Western Development Strategy and "Belt and Road" strategy would cause a certain degree of harm to the regional ecological environment. In order to assess the vulnerability of regional ecological environment, 41 soil sampling points were arranged in Altay Prefecture, and the spatial distribution map of heavy metals in soil was drawn. Among them, the content of Cu and Zn exceeded the soil background value most seriously, accounting for 28.73% and 19.37% respectively. The improved potential pollution risk index method was used to evaluate the risk of heavy metal pollution in the soil environment of Altay Prefecture. The results showed that the area of low risk areas in Altay Prefecture was the largest, accounting for 34.06%. The total area of high-risk and very high risk areas accounts for 24.98%, about 1/4 of the total area. Finally, based on multi-index factors such as topography, precipitation, soil type, soil media, vegetation types, lithology, geological disasters, heavy metal pollution, a comprehensive evaluation system of ecological environment sensitivity was constructed. The ecological environment sensitivity in Altay Prefecture was divided into four levels, and the proportion of each level area from high to low was: medium sensitive area (59.74%)＞low sensitive area (18.79%)＞high sensitive area (12.09%)＞extremely sensitive area (9.38%). Accurate assessment of the pollution risk of heavy metals and the vulnerability of ecological environment is crucial, which will provide scientific basis and theoretical support for the decision-making of relevant government agencies in Altay Prefecture.