Ephedra sinica (E. sinica) holds significant economic and medicinal importance and is predominantly found in arid areas. Due to the limitations of environmental variables, growth habits, and human activities, the production and suitability areas of E. sinica have significantly decreased, especially in the five northwestern provinces of China. In this study, 212 distribution points of E. sinica and 40 environmental variables were obtained to project the habitat suitability of E. sinica under different emission scenarios in the future. It identified precipitation in the wettest month, monthly mean of the diurnal temperature difference, and solar radiation intensity in April and July as the primary environmental factors affecting the suitability of E. sinica in the region. The areas of high, medium, and low suitability in the region cover 103,000 km2, 376,500 km2, and 486,800 km2. Under future scenarios, the suitability areas from 2021 to 2100 will decrease by 20%, with high suitability areas decreasing by 65% to 85% particularly. With comprehensive environmental variables, the suitability areas of E. sinica from 2021 to 2100 are projected, filling the gap in the projection of E. sinica suitability areas in the five northwestern provinces of China over long time period. The suitability areas show a significant decreasing trend. This research provides valuable insights into the suitability areas and crucial environmental factors, offering theoretical support for future protection and management efforts for E. sinica.