Panax notoginseng inflorescences (PNI) and leaves (PNL) are commonly used as folk medicine and food supplements. In this study, an online two-dimensional hydrophilic interaction × reversed-phase liquid chromatography coupled to linear trap quadropole mass spectrometry method was developed to determine 24 ginsenosides, including two novel compounds, in PNI and PNL extracted by water and methanol. Our data demonstrated that ginsenosides Rd, Rc, Rb2, Rb3, Rb1, Ra2, Ra1, and Ra3 in both PNI and PNL extracted by water rather than methanol can be transformed to ginsenoside F2, notoginsenoside Fe, ginsenoside Rd2, notoginsenoside Fd, gypenoside XVII, PN02, PN01, and PN03, respectively, by selectively cleaving the β-(1→2)-glucosidic linkage at the C-3 position. Ginsenoside transformation was further verified to be mediated by the proteins isolated from samples. Additionally, the two newly discovered transformed products, namely, PN02 and PN03, were prepared and identified as novel compounds by nuclear magnetic resonance. Our findings provide new insight into the importance of extraction solvents on the component profile of natural products.