The suitable habitat of endangered Ephedra species has been severely threatened and affected by climate change and anthropogenic activities; however, their migration trends and restoration strategies are still relatively understudied. In this study, we utilized the MaxEnt model to simulate the suitable habitats of five endangered Ephedra species in China under current and future climate scenarios. Additionally, we identified significant ecological corridors by incorporating the minimum cumulative resistance (MCR) model. Under the current climate scenario, the suitable area of Ephedra equisetina Bunge, Ephedra intermedia Schrenk ex Mey, Ephedra sinica Stapf, and Ephedra monosperma Gmel ex Mey comprised 16% of the area in China, while Ephedra rhytidosperma Pachom comprised only 0.05%. The distribution patterns of these five Ephedra species were primarily influenced by altitude, salinity, temperature, and precipitation. Under future climate scenarios, the suitable areas of E. equisetina, E. intermedia, and E. sinica are projected to expand, while that of E. monosperma is expected to contract. Notably, E. rhytidosperma will lose its suitable area in the future. Our identified ecological corridors showed that the first-level corridors encompassed a wider geographical expanse, incorporating E. equisetina, E. intermedia, E. sinica, and E. monosperma, while that of E. rhytidosperma exhibited a shorter length and covered fewer geographical areas. Overall, our study provides novel insights into identifying priority protected areas and protection strategies targeting endangered Ephedra species.