The secondary metabolites of different Ephedra plants are various. Therefore, the discrimination of different Ephedra plants is significant. An objective, easy-to-use, rapid and pollution-free approach is proposed for discriminating Ephedra plants of different species, habitats and picking times on the basis of diffuse reflectance Fourier transform near infrared spectroscopy (FT-NIRS) measurements and multivariate analysis. The Fourier transform near infrared diffuse reflectance spectra (NIRDRS) were acquired from 37 pulverized samples of Ephedra plants put in glass vials in the near infrared (NIR) region between 10 000 and 4000 cm −1, averaging 64 scans per spectrum at a resolution of 4 cm −1. After spectra processing and data pre-processing, spectral data were analyzed respectively with three multivariate analysis techniques: discriminant analysis (DA), self-organizing map (SOM) and back-propagation artificial neural network (BP-ANN). The proposed method could distinguish not only the Ephedra plants of three species and two habitats but also the plants picked at different times of day without special sample treatment and the use of chemical reagents. The performance indexes of the DA model were 84.2–91.9% and the prediction accuracies of both the SOM and the BP-ANN models reached 93.3–100.0%.