Phytochemical investigation on the Panax notoginseng fruits (PNF) led to the isolation of twelve compounds, including nine triterpenoid saponins (1–9) and three flavonoids (10–12). The structures of these isolates were identified on the basis of spectroscopic analysis, as well as comparisons with the data available in the literature. All compounds were firstly isolated from PNF, among them, compound 1 was firstly obtained as a natural product, compound 2 was reported for the first time in family Araliaceae, moreover, the complete 1H- and 13C- NMR spectra of this isolate was reported for the first time. Furthermore, the chemotaxonomic significance of these compounds was discussed. •Twelve compounds were firstly isolated from the Panax notoginseng fruits.•Compound 1 was firstly obtained as a natural product.•Compound 2 was reported for the first time in family Araliaceae.•These compounds enrich the chemical diversity of the family Araliaceae.