UPLC-QTOF was used to primarily characterize the ginsenosides in the leaves of P. notoginseng, and novel aglycone malonylated ginsenosides were targeted according to neutral loss of CO2 and the product ions of acetylated aglycones, m/z 517.39 protopanaxatriol (PPT) and m/z 501.40 for protopanaxadiol (PPD). Guided by LC-MS, the target compounds were enriched by liquid-liquid extraction, and isolated by column chromatography (MCI-gel and ODS) and further purified by RPLC and orthogonal HILIC. High-resolution MS, 1D and 2D-NMR were applied for structural elucidation. Eight new compounds were obtained, named as notoginsenoside L5-L12. They are all 3-OH malonylated ginsenosides, and amongst them, notoginsenoside L9-L12 are of PPT type, while notoginsenoside L5-L8 are of PPD type. Further analysis of different parts (roots, leaves, stems, and flower buds) of P. notoginseng displayed the distribution specificity, as the target compounds are detected mainly in the aerial non-medicinal parts (flowers, leaves and stems) and rarely in the underground medicinal parts (roots), indicating the targets are potential quality markers (Q-markers) to differentiate the medicinal and non-medicinal parts of P. notoginseng. This study provides a solution to discovering and isolating the aglycone malonylated ginsenosides that are Q-markers for quality control of notoginseng products.