Discrimination of species and geographical origins of traditional Chinese medicine (TCM) is essential to prevent adulteration and inferior problems. We studied Ephedra sinica Stapf, Ephedra intermedia Schrenk et C.A.Mey. and Ephedra przewalskii Bge. to investigate the relationship between inorganic element content and these three species and their geographical origins. 38 elemental fingerprints from six major Ephedra-producing regions, namely, Inner Mongolia, Ningxia, Gansu, Shanxi, Shaanxi, and Sinkiang, were determined to evaluate the importance of inorganic elements to three species and their geographical origins. The contents of 15 elements, namely, N, P, K, S, Ca, Mg, Fe, Mn, Na, Cl, Sr, Cu, Zn, B, and Mo, of Ephedra samples were measured using inductively coupled plasma mass spectroscopy. Elemental contents were used as chemical indicators to classify species and origins of Ephedra samples using a radar plot and multivariate data analysis, including hierarchical cluster analysis (HCA), principal component analysis (PCA), and discriminant analysis (DA). Ephedra samples from different species and geographical origins could be differentiated. This study showed that inorganic elemental fingerprint combined with multivariate statistical analysis is a promising tool for distinguishing three Ephedra species and their geographical origins, and this strategy might be an effective method for authenticity discrimination of TCM.