Fritillaria unibracteata is an endangered medicinal material species endemic to the Qinghai Tibet Plateau, and belongs to the national Class III endangered plant. In addition to expelling wind and removing damne, it also warms menstruation and relieves pain in clinic use of tranditional Chinese medicine. In recent years, affected by the destruction of shrubs and climate change, the habitat of F. unibracteata wild resources has been seriously damaged, indicating of great significance to predict its potential suitable habitat using MaxEnt model. The AUC values without human activities were 0.983 ± 0.013–0.988 ± 0.001, while it is 0.982 ± 0.015–0.989 ± 0.000 with human activities, justifying their applications for predicting the potential areas of F. unibracteata. Without human activities, there were 8.47 × 104 km2 of highly suitable habitats in northern Sichuan, southern Gansu and southeastern Qinghai. But the poorly, moderately and highly suitable areas of F. unibracteata have decreased to 33.8 × 104 km2, 9.66 × 104 km2 and 6.64 × 104 km2 due to human activities. Environmental variables affecting F. unibracteata distribution included the minimum temperature in the coldest month (−16.89–−4.96 °C), annual precipitation (416.64–866.96 mm), temperature annual range (24.83–31.97 °C), elevation (2879.69–3981.82 m), human footprint (2.58–23.66) and mean UV-B of highest month (7381.92–8574.27 kJ/m2). In the 2050s and 2090s, human activities would significantly reduce the highly suitable habitats of F. unibracteata. Under SSP1-2.6, SSP2-4.5 and SSP5-8.5 scenarios, the centroid would move to the low latitude area from the current position first, and then to a high latitude area. Wild resources of F. unibracteata in China can be effectively conserved based on our results.