Ephedra sinica Stapf is an important traditional medicinal plant. However, in recent years, due to climate change and human activities, its habitat area and distribution area have been decreasing sharply. In order to provide better protection for E. sinica, it is necessary to study the historical and future potential zoning of E. sinica. The maximum entropy model (MaxEnt) was used to simulate the potential geographical distribution patterns of E. sinica under historical and future climatic conditions simulated using two Shared Socio-economic Pathways. The main results were also analyzed using the jackknife method and ArcGIS. The results showed that: (1) the potential suitable distribution area of E. sinica in China is about 29.18 × 105 km2—high-suitable areas, medium-suitable areas, and low-suitable areas cover 6.38 × 105 km2, 8.62 × 105 km2, 14.18 × 105 km2, respectively—and E. sinica is mainly distributed in Inner Mongolia; (2) precipitation and temperature contribute more to the distribution of E. sinica; (3) under two kinds of SSPs, the total suitable area of E. sinica increased significantly, but the differences between 2021–2040, 2041–2060, 2061–2080, and 2081–2100 are not obvious; (4) the barycentre of E. sinica moves from the historical position to its southwest. The results show that E. sinica can easily adapt to future climates well, and its ecological value will become more important. This study provides scientific guidance for the protection, management, renewal and maintenance of E. sinica.