Co-culture fermentation is a novel technology for enhancing fermentation quality and promoting gamma-aminobutyric acid (GABA) yield. The purpose of this study was to evaluate the effects of Levilactobacillus brevis YSJ3 and Lactiplantibacillus plantarum JLSC2-6 co-culture on GABA yield, volatile and non-volatile metabolite profiles, and antioxidant activity in cauliflower byproducts. It was found that co-culture had the highest GABA yield (35.00 ± 1.15 mg/L) in fermented cauliflower stems. In total, 111 and 1264 volatile and non-volatile metabolites, respectively, were identified, of which 59 metabolites were significantly upregulated after co-culture fermentation. The results showed that 24 key upregulated metabolites were positively associated with hydroxyl radical-scavenging activity. Notably, Levilactobacills were positively correlated with the yield of GABA and key upregulated metabolites. Thus, these results suggest that Levilactobacillus brevis and Lactiplantibacillus plantarum can improve in key metabolites, GABA yield, and antioxidant activity following co-culture. This study provide a theoretical basis for developing GABA-rich cauliflower byproducts.