Continued global climate and environmental changes have led to habitat narrowing or migration of medicinal plants. Gentiana rhodantha Franch. ex Hemsl. is a medicinal plant for ethnic minorities in China, and it has a remarkable curative effect in the treatment of lung-heat cough. However, its habitat is gradually decreasing, and the species has been listed as an endangered ethnic medicine due to excessive harvesting. Here, based on CMIP6 bioclimatic data and 117 species occurrence records, the maximum entropy model (MaxEnt), combined with ArcGIS technology, was applied to predict the potentially suitable habitats for G. rhodantha under different climate scenarios. The results showed that the most critical bioclimatic variables affecting G. rhodantha are the precipitation of the warmest quarter (Bio18) and the mean temperature of the coldest quarter (Bio11). The highly suitable habitats of G. rhodantha are mainly concentrated in Belt and Road (“B&R”) countries, including China, Bhutan, and Vietnam. However, under different climate change scenarios, the fragmentation extent of suitable habitats in China will generally increase, the suitable area will show a decreasing trend as a whole, the distribution center will shift to the northeast, and the distance will increase with time. Notably, the shrinkage of the high suitability area was the most obvious for the 2081–2100 SSP585 scenario, with a total of 358,385.2 km2. These findings contribute to the understanding of the geo-ecological characteristics of this species, and provide guidelines for the conservation, management, monitoring, and cultivation of G. rhodantha.