With global warming and the intensity of human activities, the extinction trend of endangered species has increased significantly. It is of great practical significance to protect endangered plants in the Qinghai-Tibetan Plateau (QTP), especially rare and endangered trees. In this paper, 14 representative rare and endangered arbors on the QTP were selected as the research objects, and their distribution under current and future climate scenarios were modeled and the richness were analyzed, and the suitable distribution areas and priority protection areas were discussed. The results show that the suitable distribution areas of endangered arbors are mainly concentrated in the southeastern, the middle and low-elevation mountains of the QTP, where the altitude is relatively lower and the water-heat conditions are relatively better. However, the proportions of nature reserves covered in these areas are very low, forming a large number of protection gaps, which is extremely unfavorable to the protection of endangered arbors on the QTP. Based on the analyses of this paper, the valleys in the middle and lower reaches of the Yarlung Zangbo River, the Hengduan Valleys in the southeastern QTP, and the valleys in the western Sichuan Plateau in the eastern QTP are suggested as key areas that should be prioritized for planning and construction of protected areas. Nature reserves should be established in due course to improve the adaptation of endangered trees to climate change and human activities.