Abstract: In this study, we accurately collected the embryonic parenchyma cells and endocarp stone cells of Arctii Fructus at five different growth stages by laser microdissection. Quantitative analyse of caffeic acid, arctiin and arctigenin in these cells were performed using ultra-fast liquid chromatography-tandem mass spectrometry (UFLC-MS/MS). The results showed that a large amount of arctiin was produced and accumulated in embryonic parenchyma cells from the late flowering stage to mature stage, while much lower content of arctiin was produced and accumulated in endocarp stone cells at these stages. It suggested that the biosynthetic pathways of arctiin were different in embryonic parenchyma cells from endocarp stone cells of Arctii Fructus. Arctigenin was found to be produced and accumulated in both embryonic parenchyma cells and in endocarp stone cells from the late flowering stage to mature stage, but it reached a peak in endocarp stone cells at late flowering stage, then decreased slowly. The concentration of arctigenin was far less than that of arctiin regardless of embryonic parenchyma cells or endocarp stone cells. These results have validated the new method for analysis of dynamic accumulation of arctiin in Arctii Fructus by UFLC-MS/MS with frozen sections and microdissection.