Ephedra species are beneficial for environmental protection in desert and grassland ecosystems. They have high ecological, medicinal, and economic value. To strengthen the protection of the sustainable development of Ephedra, we used occurrence records of Ephedra sinica Stapf., Ephedra intermedia Schrenk et C.A. Mey., and Ephedra equisetina Bge., combined with climate, soil, and topographic factors to simulate the suitable habitat of three Ephedra based on ensemble models on the Biomod2 platform. The results of the models were tested using AUC, TSS, and kappa coefficients. The results demonstrated that the ensemble model was able to accurately predict the potential distributions of E. sinica, E. intermedia, and E. equisetina. Eastern and central Inner Mongolia, middle and eastern Gansu, and northeastern Xinjiang were the optimum regions for the growth of E. sinica, E. intermedia, and E. equisetina, respectively. Additionally, several key environmental factors had a significant influence on the suitable habitats of the three Ephedra. The key factors affecting the distribution of E. sinica, E. intermedia, and E. equisetina were annual average precipitation, altitude, and vapor pressure, respectively. In conclusion, the results showed that the suitable ranges of the three Ephedra were mainly in Northwest China and that topography and climate were the primary influencing factors.