The roots of Panax notoginseng (Burk) F. H. Chen are used as a highly valuable Chinese herbal medicine in the prevention and treatment of cardiovascular and hematological diseases. Several aerial parts of plant are usually abandoned as the wastes. Panax notoginseng inflorescence (IFO) is commonly used as a folk medicine and dietary ingredient, its fruiting stage is referred as infructescence (IFU). Owing to high chemical complexity and structural similarity of ginsenosides, the co-eluting phenomenon, especially for the isomers, is inevitable in the chromatogram, resulting in the inaccurate quantitation. A novel LC[sbnd]MS method using hybrid positive full scan and multiple reaction monitoring (MRM) modes was developed to characterize ginsenoside distribution in different architectural components of IFO and IFU. MRM was performed for the quantification of G-Ra2 and NG-Fp2, a pair of co-eluting isomers with identical negative MS and MS/MS characteristics, and full scan was conducted to quantify other investigated saponins. Our data indicate that flower buds have the highest abundance of the summed saponins, fruit pedicel and fruit pericarp, commonly considered as the useless by-products of seed processing, contain the abundant saponins. Additionally, the contents of the detected ginsenosides in these architectural components significantly increased along with their growth years. Our findings will facilitate comprehensive utilization and exploitation of P. notoginseng inflorescence and infructescence.