γ-aminobutyric acid (GABA), a non-protein amino acid, is a major inhibitory neurotransmitter within the human nervous system. Research on enhancing GABA production through the co-culture of yeast and lactic acid bacteria is limited, and the intricacies of their interactions and the mechanisms behind GABA enhancement are not fully elucidated. In this study, five yeast strains from Sichuan Pao Cai were co-cultured with Enterococcus faecium AB157 to increase GABA content, and it was found that combining E. faecium AB157 with Saccharomyces cerevisiae SC125 at a 4:1 ratio, along with 12 g/L MSG, at 35 °C, optimized GABA production to reach levels of 6.57 g/L. Within the co-culture system, there was a notable increase in both glutamate decarboxylase activity (GAD) and medium pH, while the activity of Autoinducer-2 (AI-2) remained stable. Furthermore, the cell-free supernatants (CFS) from S. cerevisiae SC125 were able to enhance GABA production by E. faecium AB157, up to 4.61 g/L. RNA sequencing revealed that the GABA biosynthetic pathways and quorum sensing (QS) in co-fermentation on E. faecium AB157 were upregulated, and the ATP synthesis and arginine deiminase pathway were downregulated compare to the pure culture of E. faecium AB157.