Methanol and water are commonly used solvents for chemical analysis and traditional decoction, respectively. In the present study, a high-performance liquid chromatography with ultraviolet detection method was developed to quantify 11 saponins in Panax notoginseng flower extracted by aqueous solution and methanol, and chemical components and anti-inflammatory effects of these two extracts were compared. The separation of 11 saponins, including notoginsenoside Fc and ginsenoside Rc, was well achieved on a Zorbax SB C18 column. This developed method provides an adequate linearity (r2  > 0.999), repeatability (RSD < 4.26%), inter- and intraday variations (RSD < 3.20%) with recovery (94.7-104.1%) of 11 saponins concerned. Our data indicated that ginsenoside biotransformation in PNF was found, when water was used as the extraction solvent, but not methanol. Specifically, the major components of Panax notoginseng flower, ginsenosides Rb1, Rc, Rb2, Rb3, and Rd, can be near completely transformed to the minor components, gypenoside XVII, notoginsenoside Fe, ginsenoside Rd2, notoginsenoside Fd, and ginsenoside F2, respectively. Total protein isolated from Panax notoginseng flower is responsible for this ginsenoside biotransformation. Additionally, methanol extract exerted the stronger anti-inflammatory effects than water extract in lipopolysaccharide-induced RAW264.7 cells. This difference in anti-inflammatory action might be attributed to their chemical difference of saponins.