Abstract: The anatomy,histochemistry and phytochemistry methods were applied in the study of the relationship between the structures of vegetative organs of one-year-old and two-year-old Scutellaria baicalensis Georgi and its effective ingredients.The results showed that the development and primary structure of the vegetative organs were the same as other dicotyledons.The baicalin was distributed in the parenchyma cells of vegetative organs and concentrated in the vascular tissue.The content of baicalin in different vegetative organs showed conspicuous difference,the highest amount was in the root,the lowest one was in the leaf and the amount in stem lay between them.This difference related to their structures.In the root of S.baicalensis,the vascular tissue in which parenchyma cells were the major elements took a major portion,so it was the reason why the highest baicalin amount was got in root.As a result,the root was the main storing sites for baicalin,which was coincident with the tradition,i.e.the root of S.baicalensis Georgi was used as medicinal parts.In addition,the highest baicalin content was detected in the two-year-old root at the early stage of vegetative growth,so it should be better to harvest in spring.