Abstract: To investigate the nutritional characteristics of different specialty millet varieties, this study selected the local specialty variety Qingyang Jiugu (QYJG) and the modern elite cultivar Longgu 23 (LG23) as research subjects, systematically comparing their differences in nutritional quality and metabolite profiles. The physicochemical components of both varieties were measured, and their metabolites were analyzed using widely targeted metabolomics technology. Metabolite characteristics were analyzed by principal component analysis, orthogonal partial least squares discriminant analysis, cluster analysis and metabolic pathway analysis. Results showed that the amylose content of QYJG was only 0.91%, indicating that it was a typical waxy millet variety. QYJG exhibited higher contents of unsaturated fatty acids (90.85%), polyphenols (1.00 mg GAE/g) and polysaccharides (7.66 mg/g) than LG23 (P<0.05), along with a relatively favorable fatty acid composition. In contrast, the contents of flavonoids (15.72 mg RE/g), essential amino acids (96.88 mg/kg) and total amino acids (1765.72 mg/kg) in LG23 were significantly higher than those in QYJG (P<0.01). LG23 also contained abundant levels of branched-chain amino acids and limiting amino acids, which confered a significant advantage in amino acid synthesis. A total of 1408 metabolites were identified in QYJG and LG23, primarily consisting of lipids, alkaloids, flavonoids, amino acids and their derivatives. 587 significantly differential metabolites were screened, with 366 up-regulated in QYJG and 221 up-regulated in LG23. These differential metabolites were mainly involved in pathways related to the biosynthesis and metabolic pathways of secondary metabolites, amino acids, carbohydrates, vitamins and cofactors, as well as lipid. Lipid and carbohydrate metabolic pathways were more active in QYJG, which may contribute to its antioxidant stability and low glycemic properties. LG23 exhibited enhanced amino acid and flavonoid metabolic pathways, highlighting its superior antioxidant capacity and nitrogen metabolism efficiency. This study revealed the differences in nutritional quality and metabolic profiles between QYJG and LG23 from the perspectives of physicochemical properties and metabolomics, which provided a theoretical basis for precise breeding of millet varieties and the development and utilization of related products.