Abstract: Acanthopanax senticosus (Rupr.et Maxim.) Harms. (AS) is a medicinal plant which mainly distributes in Northeastern area of China, due to the widely utilization in clinical and pharmaceutical industry, the wild resource of the plant is limited, the cultivation of the plant is in needed currently. Therefore it is of importance to select a medicinal priority for cultivating from two different sexual type of AS. In the present study, UPLC-MS technology-based metabolic profiles was used to discriminate phenotypes. By processing the metabolomic data with principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal projection to latent structures (OPLS) analysis, eleven secondary metabolites were found to be responsible for classing the two varieties of Acanthopanax senticosus, they might be taken as potential biological markers of sexual type. These marker metabolites include flavone, coumarin, terpenes and organic acids, which are the main active constituents related to the therapeutic effects of Acanthopanax senticosus. Among these valuable secondary metabolites, flavone, anthraquinone and organic acids are highly expressed in short capillament Acanthopanax senticosus, while coumarin and terpenoid are highly expressed in the long capillament variety. As a result, by monitoring these highly expressed metabolites and through selective cultivation, an Acanthopanax senticosus with higher amounts of medicinally relevant constituents could be created.