Climate change has a significant impact on species distribution, especially for the relict plants. Euptelea pleiosperma is a type of tertiary relict plant. This plant shows a decreasing trend in population size, and it is on the edge of extinction given the background of climate change. Understanding the change in suitable habitats of E. pleiosperma will provide significant academic value for investigating species conservation and sustainable development. According to the 236 distribution records of E. pleiosperma in China, and 11 environmental factors, the optimal model was selected from MaxEnt, BIOCLIM, and DOMAIN models, aiming to estimate the future potential suitable habitats and exploring the major environmental factors influencing the distribution of E. pleiosperma. By comparison, the BIOCLIM model was the optimal for estimation, since it achieved the highest precision and the lowest standard error. Our results demonstrated that temperature was the most important factor affecting the suitable habitats of E. pleiosperma, followed by precipitation and altitude. Under the medium- and high-emission scenarios, the future suitable habitats of E. pleiosperma will migrate northward to the high-latitude areas, whereas those under the low-emission scenario will migrate southward to the low-latitude areas. During 2041–2060, the suitable habitat areas will present a positive trend, while those during 2081–2100 will exhibit a negative trend to varying degrees. Consistent with the above results, it is advisable to establish natural reserves and seed resource banks of E. pleiosperma in the current high suitability areas, as well as to provide artificial assistance to guide its migration to the high suitability areas under the future climate scenarios. The findings in this research not only reveal the response of suitable habitats of E. pleiosperma to climate change but also lay a reliable foundation for its population resource conservation and sustainable development.