Abstract: Using underground partial roots and aboveground stems, leaves and fruits of Panax notoginseng as materials. The difference of flavonoids in different parts of P. notoginseng were detected by LC-MS/MS technology. PCA analysis, OPLS-DA analysis and repeated correlation evaluation of samples were carried out for detected metabolites by using the MVDB and metabolism database. Then, KEGG database was used to annotate the metabolic pathways involved in differential metabolites to screen out differential metabolites and analyze their differences in different parts. The findings indicated that a total of 149 differential metabolites were detected in 4 sites, the number of flavonoids in P. notoginseng is S(stem) 138 > F(fruit) 134 > L(leaf) 127 > R(root) 120. Leaves, fruits, and stems contain more flavonoids than roots; using the underground partial roots as the control, comparing the differences with aerial stems, leaves and fruit. Among them, in the F vs R group, 6 were selected(epigallocatete catechin, planstorage side, copol-3′-O-glucoside, etc.), down-regulated 14(quercetin, geranin-3-O-glucoside, phenol-8-C-glucoside, etc.); in the L. vs. R group, up-regulated 2(isrhamin-3-O-arabinoglyside, antochatechin gallate), down-regulated 18(peony anthocyanin-3-O-glucoside, sanannin-3-O-glucuronside, myricetin-3-O-galactoside, etc.); in the S vs. R group, 4 genes were up-regulated(4′, 5,7-trihydroxyl-3′, 6-dimethoxyflavones(palm vecuthrin), flat storage side, kaempferol-7-O-glucoside,etc.), down-regulated 16(quercetin,sanonesin-3-O-glucuronide, myricetin-3-O-galactoside, etc.); leaves, fruits and stems contain a large number of different secondary metabolites with different characteristics and roots. For example, geranium-3-O-glucoside, morning glory-3-O-rutcoside, isrhamin-3-O- (2′′-O-xylosyll) glucoside can be used as landmark differences differentiating roots. The flavonoids active substances in different parts of P. notoginseng varied greatly, the relative content of flavonoids in different tissue parts of Panax notoginseng was higher in leaves, fruits and stems, and lower in roots than other parts.