In this study, the effect of luxS, a key gene involved in quorum sensing, on the characteristic flavor of yogurt and its molecular mechanisms during the cofermentation of yogurt with engineered probiotics was investigated. The luxS gene overexpression strain was constructed by the homologous recombination technique, and its effect on the expression of population sensing signaling molecules and luxS gene was determined by bioluminescence and quantitative real-time PCR, and finally, headspace solid-phase micro extraction-GC-MS (HS-SPME-GC-MS) and metabolomics were used to determine the mechanism of its effect on the characteristic flavor of yogurt. The results demonstrated that the overexpression strains of Lactobacillus acidophilus CICC 6074-pMG36e-luxS and Lactobacillus helveticus R0052-pMG36e-luxS were successfully constructed. The expression of the luxS gene was upregulated by 2.25-fold and 3.16-fold, respectively. Compared with the wild-type strains, yogurt fermented by the overexpression strains showed a significant increase in AI-2 content, acidity, viable bacterial count, and protein hydrolysis, whereas pH, water-holding capacity, and hardness were significantly reduced. The HS-SPME-GC-MS results revealed the presence of 31 volatile flavor substances in yogurt. Among them, benzaldehyde (almond and burned sugar flavors), 2,4-dimethyl- (almond, cherry, and naphthalene flavors), dibutyl phthalate (a faint aromatic odor), and n-decanoic acid (rancid and fatty notes) were identified as the key differential flavor substances mediated by the luxS gene. Metabolomics results showed that the luxS gene mediates the production of organic acids in yogurt through arginine and proline metabolism, phenylalanine metabolism, and tryptophan metabolism. This study provides a theoretical basis for a deeper understanding of the molecular mechanisms underlying yogurt flavor formation.