Panax notoginseng(P. notoginseng) has excellent medicinal and food dual-use characteristics. However,P. notoginsengwith a unique origin label has become the target of fraud because of people confusing or hiding its origin. In this study, an untargeted nuclear magnetic resonance (NMR)-based metabolomics approach was used to discriminate the geographical origins ofP. notoginsengfrom four major producing areas in China. Fifty-two components, including various saccharides, amino acids, saponins, organic acids, and alcohols, were identified and quantified through the NMR spectrum, and the area-specific geographical identification components were further screened.P. notoginsengfrom Yunnan had strong hypoglycemic and cardiovascular protective effects due to its high acetic acid, dopamine, and serine content, whileP. notoginsengfrom Sichuan was more beneficial for diseases of the nervous system because of its high content of fumarate.P. notoginsengfrom Guizhou and Tibet had high contents of malic acid, notoginsenoside R1, and amino acids. Our results can help to distinguish the geographical origin ofP. notoginsengand are readily available for nutritional recommendations in human consumption.