Abstract: The application of HPLC-NMR-MS hyphenated technique in the structural identification of trace substances from complex mixtures and the identification of endogenous and exogenous substances in the establishment process of metabolic profiling have become effective analytical tools in pharmaceutical chemistry, pharmacological and pharmacokinetic studies of active substances from natural products. Metabolomics method based on NMR technology can accurately portray metabolic phenotypes with the characteristics of diseases and a variety of disease-related pathways, and it can greatly enrich and supplement the traditional disease evaluation methods. So it can be used for pharmacological studies of active substances from natural products, such as toxicological studies, the dose optimization, active substances screening and pharmacodynamic evaluation. Hyphenated technique associated with metabolomics method based on NMR technology will accelerate the speed of the discovery of active substances from natural products, and improve the efficiency of their pharmacological evaluation.