Wetland ecosystems in the Qinghai-Tibet Plateau (QTP), the region with the richest biodiversity and the most important ecological barrier function at high altitudes, are highly sensitive to global change, and wetland plants, which are important indicators of wetland ecosystem structure and function, are also threatened by wetland degradation. Therefore, a comprehensive study of changes in the geographical distribution pattern of plant diversity, as well as species loss and turnover of wetlands in the QTP in the context of global climate change is of great importance for the conservation and restoration of wetland ecosystems in the QTP. In this study, species turnover and loss of 395 endemic wetland plants of the QTP were predicted based on the SSP2-4.5 climate change scenarios. The results showed that there were interspecific differences in the effects of climate change on the potential distribution of species, and that most endemic wetland plants would experience range contraction. Under the climate change scenarios, the loss of suitable wetland plant habitat is expected to occur mainly in parts of the southern, north-central and north-western parts of the plateau, while the gain is mainly concentrated in parts of the western Sichuan Plateau, the Qilian Mountains, the Three Rivers Source Region and the northern Tibetan Plateau. Overlaying the analysis of priority protected areas with the established protected areas in the QTP has resulted in the following conservation gaps: the eastern Himalayan region, midstream of the Yarlung Zangbo River, the transition zone between the northern Tibetan Plateau and the Hengduan Mountains, Minshan-Qionglai mountain, Anyemaqen Mountains (southeast) to Bayankala (southeast) mountains, the southern foothills of the Qilian Mountains and the northern Tibetan Plateau region. In the future, the study of wetland plant diversity in the QTP and the optimisation of protected areas should focus on the conservation gaps. This study is of great importance for the study and conservation of wetland plant diversity in the QTP, and also provides a scientific basis for predicting the response of wetland plants to climate change in the QTP.