[Objective] To examine the effect of endophytic fungi ALl2 (Gilmaniella sp.) on metabolites distribution in organs of Atractylodes lancea. [Method] Endophytic fungi ALl2 was inoculated on Atraetylodes lancea plantlets in tissue culture, and the distribution of cellulose, hemicellulose, lignin, soluble sugar in leaves and roots of the inoculated group were detected. The weight of leaves and roots were compared. Gas Chromatography was used to analyze the volatile oil components. [Result] Compared with the control group, the average fresh weight and dry weight of leaves and roots of A. lancea which had been symbiosed with ALl2 increased significantly. The content of lignin and soluble sugar increased in the leaves of the inoculated group, and the content of cellulose, hemicellulose, lignin, soluble sugar and volatile oil also increased in roots. [Conclusion] The results indicate that symbiosed with ALl2 is benefit for the development of A. lancea roots and can promote the transfer and accumulation of the medicinal components to the roots.