In this study, the microbial interactions among cocultures of Streptococcus thermophilus (St) with potential probiotics of Bifidobacterium animalis ssp. lactis (Ba) and Lactiplantibacillus plantarum (Lp) in fermented milk were investigated during a storage period of 21 d at 4°C, in terms of acidifying activity (pH and titratable acidity), viable counts, and metabolites. A nontargeted metabolomics approach based on ultrahigh-performance liquid chromatography coupled with mass spectrometry was employed for mapping the global metabolite profiles of fermented milk. Probiotic strains cocultured with St accelerated milk acidification, and improved the microbial viability compared with the single culture of St. The St-Ba/Lp treatment manifested a higher bacteria viability and acidification ability in comparison with the St-Ba or the St-Lp treatment. Relative quantitation of 179 significant metabolites was identified, including nucleosides, AA, short peptides, organic acids, lipid derivatives, carbohydrates, carbonyl compounds, and compounds related to energy metabolism. The principal component analysis indicated that St treatment and coculture treatments displayed a complete distinction in metabolite profiles, and Lp had a larger effect than Ba on metabolic profiles of fermented milk produced by cofermentation with St during storage. The heat map in combination with hierarchical cluster analysis showed that the abundance of metabolites significantly varied with the starter cultures over the storage, and high abundance of metabolites was observed in either St or coculture samples. The St-Ba/Lp treatment showed relatively high abundance for the vast majority of metabolites. These findings suggest that the profile of the metabolites characterizing fermented milk samples may depend on the starter cultures, and incorporation of probiotics may considerably influence the metabolomic activities of fermented milks.