Astragali radix (AR), known in China as huangqi, is commonly used in traditional Chinese medicine. Water soluble extractive (WSE) values play an important role in the quality evaluation of herbal drugs. In this study, WSE of wild and cultivated AR were compared systematically. The WSE value of cultivated AR was significantly higher than that of the wild AR, and their UV-absorbance in the range of 250–400 nm was also different. The chemical compositions of different WSE were further compared by 1 H NMR spectroscopy combined with multivariate analysis. Results from the principal component analysis and the hierarchical cluster analysis showed a clear separation between the WSEs of wild and cultivated AR. The differential metabolites responsible for the separation were identified by orthogonal projections to latent structures discriminant analysis and recursive support vector machine. The WSE of wild AR contained more arginine, valine, threonine, asparagine, succinate, and glutamine, while the cultivated AR contained more sucrose. Thus, the WSE can be used as a simple and reliable method for discrimination of wild and cultivated ARs, and the results obtained in this study extend the potential use of WSE in the quality evaluation of herbal drugs.