Climate change is a vital driver of biodiversity patterns and species distributions, understanding how organisms respond to climate change will shed light on the conservation of endangered species. In this study, the MaxEnt model was used to predict the potential suitable area of 12 threatened medicinal plants in the QTP (Qinghai-Tibet Plateau) under the current and future (2050s, 2070s) three climate scenarios (RCP2.6, RCP4.5, RCP8.5). The results showed that the climatically suitable habitats for the threatened medicinal plants were primarily found in the eastern, southeast, southern and some part of the central regions on the QTP. Moreover, 25% of the threatened medicinal plants would have reduced suitable habitat areas within the next 30-50 years in the different future global warming scenario. Among these medicinal plants, FP (Fritillaria przewalskii) would miss the most habitat (97.1%), while the RAN (Rhododendron anthopogonoides) would miss the least habitat (0.30%). Nevertheless, 41.6% of the threatened medicinal plants showed an increase in their future habitat area because of their physiological characteristics which are more adaptable to a wide range of climate. The climatic suitable habitat for 50% of the threatened medicinal plants would migrate to higher altitudes or higher latitudes regions. This study provides a data foundation for the conservation of biodiversity and wild medicinal plants on the QTP.