A discriminant LC/MS quantitative analysis of ephedrine (EP) and pseudoephedrine (PEP) in Ephedrae herba was performed. Aerial parts of three Ephedra species were separated into internodes and extracted using Finger Masher with minimum loss. The contents of EP and PEP were measured by LC/MS/MS using the multiple reaction monitoring (MRM) method. Their contents in old-year branches were lower than those current-year branches and tended to be higher in the middle part than in the tip of each branch. The content ratio of EP and PEP was reversed in some branches depending on their extent of growth. In E. sinica , the contents were low at the first internode closest to the central main stem at each branch. The contents drastically increased from the second internode and were highest at the third internode. There was a strong correlation between the internode distance and alkaloid (EP + PEP) contents. The distribution of alkaloids in one internode was examined and the results showed that the part closest to the node had the lowest contents. Graphic abstract