Abstract: NMR-based metabolomics technique has been applied to botanical studies in recent years. The plant metabolites are complicated and various, metabolomics method can detect the global metabolomic profile of the plant to track valuable metabolites, and provide information for the research of plant physiology, metabolic pathways and functional genes. This paper reviews the application of NMR-based metabolomics technique in medicinal plants, including the biosynthetic mechanism and production of secondary metabolites, the improvement of yield or quality of medicinal plants, the development of effective active ingredient, the identification of medicinal plant species, and the quality control of herbal medicine. In addition, the potential development of this technique in future is discussed.