High quality and nutritional benefits are ultimately the desirable features that influence the commercial value and market share of broad bean (Vicia faba L.). Different cultivars vary greatly in taste, flavor, and nutrition. However, the molecular basis of these traits remains largely unknown. Here, the grain metabolites of the superior Chinese landrace Cixidabaican (CX) were detected by a widely targeted metabolomics approach and compared with the main cultivar Lingxiyicun (LX) from Japan. The analyses of global metabolic variations revealed a total of 149 differentially abundant metabolites (DAMs) were identified between these two genotypes. Among them, 84 and 65 were up- and down-regulated in CX compared with LX. Most of the DAMs were closely related to healthy eating substances known for their antioxidant and anti-cancer properties, and some others were involved in the taste formation. The KEGG-based classification further revealed that these DAMs were significantly enriched in 21 metabolic pathways, particularly in flavone and flavonol biosynthesis. The differences in key secondary metabolites, including flavonoids, terpenoids, amino acid derivates, and alkaloids, may lead to more nutritional value in a healthy diet and better adaptability for the seed germination of CX. The present results provide important insights into the taste/quality-forming mechanisms and contributes to the conservation and utilization of germplasm resources for breeding broad bean with superior eating quality.