Located in southern Qinghai Province in China, Sanjiangyuan is the source area for the Yangtze River, Yellow River, and Lancang River, and a worldwide biodiversity hotspot. Sanjiangyuan was degraded through human disturbance and climate change, which has led to a dramatic loss of the biodiversity of rangeland resources. We conducted field surveys based on species coordinates during 2014 and 2015. We used the MaxEnt model to predict distribution of 40 endangered plant species in Sanjiangyuan using the species coordinate data and bioclimatic data collected from the WorldClim database. From this, we obtained hotspots of endangered plant species in Sanjiangyuan under current and future climatic conditions. Results showed that hotspot areas of endangered plant species in Sanjiangyuan estimated using the MaxEnt model were approximately 89,438 km~2, and mainly located in the east and south of the reserve. Among these hotspots, those that included more than 30 endangered plant species totalled 485 km~2, and were mainly found in Nangqian County, Yushu City, Banma County, Jiuzhi County, and Henan County. The climate will become warmer and wetter in Sanjiangyuan in the future, which would benefit biodiversity and expand hotspot areas to the northwest. However, problems associated with planning the reserve remain. Nearly 4,423 km~2 of hotspot areas have not been protected in the key reserve, including in Nangqian County, Yushu City, Banma County, Jiuzhi County, and Henan County. In these areas grazing is permitted, which might lead to human disturbances. We suggest policy makers focus more attention on these areas and increase conservation efforts.