Although there are many reports of fossil Ephedraceae, whole plant fossil record remains rare. Due to a lack of trust on partially preserved fossil materials, scholars working on molecular clock proposed a recent origin of Ephedra and cast doubt on the earlier origin time of Ephedraceae. To better the understanding on this interesting group, here we report whole plants of Ephedra hongtaoi sp. nov. (Ephedraceae, Gnetales) from the Yixian Formation (Early Cretaceous) in western Liaoning, China. These whole plants of Ephedra demonstrate clearly the characters of Ephedra, including shrubby growth habit, decussate branching pattern, and terminal ovuliferous unit with micropylar tube. The whole-plant preservation of the fossils provides more convincing fossil evidence of Early Cretaceous Ephedra, helps to resolve the controversy over the origin time of Ephedra, and sheds light on the whole plant morphology, growth habit, ecology and evolution of Ephedraceae.