Microbial metabolism influences the physicochemical properties and flavor compound formation in fermented milk during fermentation. Streptococcus thermophilus is one of the primary fermentation strains used in fermented milk production. Herein, we investigated the fermentation characteristics, flavor profiles, and associated metabolic mechanisms of Streptococcus thermophilus JM66 in milk matrix through multi-stage dynamic monitoring and multi-omics techniques. A total of 66 volatile metabolites were identified across three fermentation stages of S. thermophilus JM66, with ketones (such as acetoin and nonanone) being the predominant flavor metabolites in the fermented milk. Metabolomic analyses revealed an increase in pyruvic acid, L-lactic acid, 2-hydroxybutyric acid, D-proline, and L-tyrosine, alongside a decrease in D-arginine, L-aspartic acid, and acetoacetyl-CoA, which were enriched in pyruvate metabolism, butanoate metabolism, amino acid metabolism and fatty acid metabolism. Furthermore, integrating transcriptomic results, high expression of LDH, budC and genes related to glycolysis, urea cycle and fatty acid biosynthesis promoted compound metabolism and flavor development. This comprehensive analysis of S. thermophilus JM66 provides a theoretical foundation for its future application as a starter culture or in strain mutagenesis aimed at enhancing fermentation characteristics.