Tree species in mountainous areas are expected to shift their distribution upward in elevation in response to climate change, calling for a potential redesign of existing protected areas. This study aims to predict whether or not the distributions of two high-mountain tree species, Abies (Abies kawakamii) and Tsuga (Tsuga chinensis var. formosana), will significantly shift upward due to temperature change, and whether current protected areas will be suitable for conserving these species. Future temperature change was projected for 15 different future scenarios produced from five global climate models. Shifts in Abies and Tsuga distributions were then predicted through the use of species distribution models (SDMs) which included occurrence data of Abies and Tsuga, as well as seasonal temperature, and elevation. The 25 km × 25 km downscaled General Circulation Model (GCMs) data for 2020–2039 produced by the Taiwan Climate Change Projection and Information Platform was adopted in this study. Habitat suitability in the study area was calculated using maximum entropy model under different climatic scenarios. A bootstrap method was applied to assess the parameter uncertainty of the maximum entropy model. In comparison to the baseline projection, we found that there are significant differences in suitable habitat distributions for Abies and Tsuga under seven of the 15 scenarios. The results suggest that mountainous ecosystems will be substantially impacted by climate change. We also found that the uncertainty originating from GCMs and the parameters of the SDM contribute most to the overall level of variability in species distributions. Finally, based on the uncertainty analysis and the shift in habitat suitability, we applied systematic conservation planning approaches to identify suitable areas to add to Taiwan’s protected area network.