Cichoric acid is the main phenolic compound in the root and rhizome of the medicinal part, Echinacea purpurea that is known for possessing immune enhancing characteristics. In this study, we analysis the the synthesis and storage sites of phenolic compound in E. purpurea. We used fluorescent microscopy, transmission electron microscopy, cytochemical and immunocytochemical localization to observe the distribution of phenolic compounds. Our results show that the phenolic compounds were mostly distributed in the cortex parenchyma cells, vascular parenchyma cells and pith parenchyma cells in the root and rhizome, and mainly present in the vacuoles, large intercellular spaces and their surrounding cell walls. No phenolic compounds were observed in the cytoplasm and the organelles. We concluded that the phenolic compounds were synthetized in the cortex parenchyma cells, vascular parenchyma cells and pith parenchyma cells in the root and rhizome, and stored in the vacuoles of parenchyma cells. The above results provided significantly cytological information for further approaching the metabolic regulation and transfer pathways of phenolic compounds in biochemistry and molecular biology.