Saussurea medusa is a rare alpine plant with significant medicinal value. To better understand the changes in its habitat in the context of climate change, this study used an optimized MaxEnt model to predict the current and future habitat of S. medusa under four shared socioeconomic pathways (SSPs) across three time periods (current, mid-century, and end-century) based on three climate system models. The results showed that the suitable habitat of S. medusa is mainly located in the southern and eastern parts of the Qinghai-Xizang Plateau (QXP), exhibiting a fragmented distribution pattern. The future suitable area of S. medusa is projected to decrease significantly by 42.5% to 96.7%, accompanied by a southward shift in its centroid and an upward shift in altitude. The study found that the highest temperature in the warmest month is the most important environmental factor affecting the distribution of S. medusa. This species is highly sensitive to climate change and requires urgent protection measures. Priority should focus on strengthening habitat protection in the southeastern Qinghai-Xizang Plateau, where some stable habitats remain outside protected areas. Expanding population monitoring, promoting ex-situ conservation, enhancing public education, and encouraging community involvement are essential. Additionally, as a medicinal plant, alternative strategies are needed to curb overharvesting of wild resources.