Sea buckthorn (Hippophaë; Elaeagnaceae) berries are widely consumed in traditional folk medicines, nutraceuticals, and as a source of food. The growing demand of sea buckthorn berries and morphological similarity of Hippophaë species leads to confusions, which might cause misidentification of plants used in natural products. Detailed information and comparison of the complete set of metabolites of different Hippophaë species are critical for their objective identification and quality control. Herein, the variation among seven species and seven subspecies of Hippophaë was studied using proton nuclear magnetic resonance (1H NMR) metabolomics combined with multivariate data analysis, and the important metabolites were quantified by quantitative 1H NMR (qNMR) method. The results showed that different Hippophaë species can be clearly discriminated and the important interspecific discriminators, including organic acids, L-quebrachitol, and carbohydrates were identified. Statistical differences were found among most of the Hippophaë species and subspecies at the content levels of the aforementioned interspecific discriminators via qNMR and one-way analysis of variance (ANOVA) test. These findings demonstrated that 1H NMR-based metabolomics is an applicable and effective approach for simultaneous metabolic profiling, species differentiation and quality assessment.