In the present paper, a fast and economical HPLC method [on a Phenomenex Polar-RP column with a solution of (phosphoric acid:triethylamine:dibutylamine:water = 0.40:0.1:0.2:499.3) and methanol] is developed, and applied for the determination of norephedrine, norpseudoephedrine, ephedrine (E), pseudoephedrine (PE) and methylephedrine (ME) in 64 samples of three species from main habitats in China. Quantitation data showed that total alkaloid content in Ephedra equisetina Bge. (2.708 ± 0.642%) is higher than that in E. sinica Stapf. (1.365 ± 0.624%) and E. intermedia Schrenk et C. A. Mey. (1.537 ± 0.746%), but the range of total alkaloid content in each species is so wide that the ranges of the three species greatly overlap. The contents of E, PE and ME are different among the three species. The ratio E/total alkaloid content and ratio E/PE as well as E and ME contents can be used for identification of E. sinica, E. intermedia and E. equisetina from one another.