Abstract: In order to study the metabolites difference in different organs of native tea plant Duyun Maojian, through qualitative and quantitative analysis on the metabolites among leaf, stem and root, a total of 504 metabolites were identified, and 205 different metabolites between leaf and root were obtained by principal component analysis（PCA）, orthogonal partial least squares discrimination analysis（OPLS-DA）, and fold change（FC）. The down-regulated metabolites in root were mainly involved in flavonoid biosynthesis, flavonol biosynthesis, and anthocyanin biosynthesis et al, which mainly determine the astringency of the tea. Caffeine, amino acids and various sugar metabolisms made tea taste bitter, fresh, and sweet, respectively. The 112 differential metabolites between leaf and stem were mainly enriched in glutathione, arginine and proline metabolism, pentose and glucuronic acid conversion pathways.