Simple SummaryClimate change is one of the most significant drivers of habitat loss and species extinction, particularly montane endemic species such as Juniper trees, which are restricted to unique habitats. Therefore, assessing the impact of climate change on the extinction risk of species is a promising tool or guide for species conservation planning. The loss in species habitat due to global warming indicates the level of extinction or endangerment. Predictions of suitable habitats are outputs from assessment analysis. This will help conservationists discover new populations of endemic species and help raise the awareness of local people to save and rescue these endangered species.Climate change is an important driver of biodiversity loss and extinction of endemic montane species. In China, three endemic Juniperus spp. (Juniperus pingii var. pingii, J. tibetica, and J. komarovii) are threatened and subjected to the risk of extinction. This study aimed to predict the potential distribution of these three Juniperus species under climate change and dispersal scenarios, to identify critical drivers explaining their potential distributions, to assess the extinction risk by estimating the loss percentage in their area of occupancy (AOO), and to identify priority areas for their conservation in China. We used ensemble modeling to evaluate the impact of climate change and project AOO. Our results revealed that the projected AOOs followed a similar trend in the three Juniperus species, which predicted an entire loss of their suitable habitats under both climate and dispersal scenarios. Temperature annual range and isothermality were the most critical key variables explaining the potential distribution of these three Juniperus species; they contribute by 16–56.1% and 20.4–38.3%, respectively. Accounting for the use of different thresholds provides a balanced approach for species distribution models’ applications in conservation assessment when the goal is to assess potential climatic suitability in new geographical areas. Therefore, south Sichuan and north Yunnan could be considered important priority conservation areas for in situ conservation and search for unknown populations of these three Juniperus species.