The Saussurea species, renowned for its biodiversity and medicinal significance in high-elevation regions, faces endangerment due to climate change and human activities. Despite this, conservation research on Saussurea has been limited. To fill the knowledge gap, this study employed the optimized MaxEnt model to simulate Saussurea's habitat suitability and analyze key environmental factors influencing its distribution. Additionally, considering the sensitivity of Saussurea habitats to climate change, this research also simulated the changes in suitable habitat and distribution centroid shifts of Saussurea under different climate scenarios (SSP126, SSP245, SSP370, and SSP585) for the periods 2040s, 2060s, 2080s and 2100s. Findings indicated that Saussurea's suitable habitat was primarily located in the Qinghai-Tibet Plateau, notably within the Himalayas and Hengduan Mountains. The areas of extremely and moderately suitable habitats were 1.106 × 10⁵ km2 and 3.436 × 10⁵ km2, respectively. Elevation, Isothermality (Bio3), and Temperature Annual Range (Bio7) were identified as the main environmental factors. Future projections suggest severe habitat fragmentation and a decrease in suitable habitat areas. By 2100, the total area of suitable Saussurea habitat will decrease under the SSP126, SSP245, SSP370, and SSP585 scenarios to 8.658 × 10⁵ km2, 6.971 × 10⁵ km2, 5.811 × 10⁵ km2, and 5.979 × 10⁵ km2, respectively. Additionally, a slight southeastward shift in the distribution centroid was observed. This study is expected to provide guidance for the conservation of Saussurea and alpine plant biodiversity.