Hemp seed is an important food and medicine source in Bama County, Guangxi Province, China, where has been renowned as the Land of Centenarians and Holy Land of Chinese Longevity. In order to clarify the metabolic characteristics of hemp seeds and analyze their medicinal and nutritional value, the metabolites and relative contents of hemp seeds in seven villages in Bama County were quantified by a widely targeted metabolomics method based on ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS). A total of 1021 metabolites were identified, including 177 flavonoids, 156 phenolic acids, 134 lipids, 113 amino acids and derivatives, 106 alkaloids, 85 organic acids, 65 nucleotides and derivatives, 39 lignans and coumarins, 12 terpenoids and 7 tannins. Then differential metabolite analysis and weighted gene correlation network analysis (WGCNA) were performed, and the key metabolites of each module were determined by cytoscape software. Finally, DPPH free radical scavenging experiment was carried out. The metabolomics data and analysis results of this study provide a theoretical basis for the development of hemp seed industry in food production and medical research in Bama.