Due to the problem of mixing use of the root and the rhizome of the Atractylodes,we provided a method to distinguish them based on Pharmacognosy including characters,microstructure,physical and chemical nature of the root and rhizome of Atractylodes.Microscopic identification of pharmacognosy method was used to observe the root and rhizome of Atractylodes characteristics in the organization of the difference.By UV and TLC methods to compare in the chemical composition of the differences.Root and rhizome of Atractylodes,there was a significant difference in tissue characteristics,but no significant difference in the chemical composition.Therefore,using microscopic pharmacognosy method,the two can be confidently identified.