Identification of the origins of Panax ginseng has been issued in Korea scientifically and economically. We describe a metabolomics approach used for discrimination and prediction of ginseng roots from different origins in Korea. The fresh ginseng roots from six ginseng cooperative associations (Gangwon, Gaeseong, Punggi, Chungbuk, Jeonbuk, and Anseong) were analyzed by UPLC-MS-based approach combined with orthogonal projections to latent structure-discriminant analysis multivariate analysis. The ginsengs from Gangwon and Gaeseong were easily differentiated. We further analyzed the metabolomics results in subgroups. Punggi, Chungbuk, Jeonbuk, and Anseong ginseng could be easily differentiated by the first two orthogonal components. As a validation of the discrimination model, we performed blind prediction tests of sample origins using an external test set. Our model predicted their geographical origins as 99.7% probability. The robust discriminatory power and statistical validity of our method suggest its general applicability for determining the origins of P. ginseng samples.