Climate change has led to shifts in species distribution and become a crucial factor in the extinction of species. Increasing average temperatures, temperature extremes, and unpredictable weather events have all become a part of a perfect storm that is threatening ecosystems. Higher altitude habitats are disproportionately affected by climate change, and habitats for already threatened specialist species are shrinking. The Siberian ibex, Capra sibirica, is distributed across Central Asia and Southern Siberia and is the dominant ungulate in the Pamir plateau. To understand how climate change could affect the habitat of Siberian ibex in the Taxkorgan Nature Reserve (TNR), an ensemble species distribution model was built using 109 occurrence points from a four-year field survey. Fifteen environmental variables were used to simulate suitable habitat distribution under different climate change scenarios. Our results demonstrated that a stable, suitable habitat for Siberian ibex was mostly distributed in the northwest and northeast of the TNR. We found that climate change will further reduce the area of suitable habitat for this species. In the scenarios of RCP2.6 to 2070 and RCP8.5 to 2050, habitat loss would exceed 30%. In addition, suitable habitats for Siberian ibex will shift to higher latitudes under climate change. As a result, timely prediction of the distribution of endangered animals is conducive to the conservation of the biodiversity of mountain ecosystems, particularly in arid areas.