In this study, the effects of adding glutamate (Glu), glutamine (Gln), aspartate (Asp), and asparagine (Asn) on the flavor formation of Huangjiu were investigated, and the effect of Gln concentration on the quality, microbial community structure, and flavor development of Huangjiu was further explored. Varied Gln concentrations influenced yeast growth, sugar utilization, microbial communities, and quality attributes. Additional Gln promoted yeast cell counts and sugar depletion. It increased the complexity of bacterial co-occurrence networks and reduced the impact of stochastic processes on assembly. Correlation analysis linked microorganisms to flavor compounds. Isolation experiments verified the role of Saccharomyces cerevisiae, Aspergillus chevalieri, Bacillus altitudinis, and Lactobacillus coryniformis in flavor production under Gln conditions. This research elucidated the microbiological mechanisms by which amino acid supplementation, especially Gln, enhances Huangjiu quality by modulating microbial metabolic functions and community dynamics during fermentation. This research is significant for guiding the production of Huangjiu and enhancing its quality.