Abstract:[Background] In the fermentation of the upper-layer fermented grains of Nongxiangxing Baijiu, there are widespread issues such as low raw material utilization rate and poor flavor quality. [Objective] To improve the yield and quality of Nongxiangxing Baijiu from the upper-layer fermented grains. [Methods] In this study, functional microbiomes (with high yields of amylase and ester compounds) were used for enhanced fermentation. [Results] The results showed that the enhancement with the functional microbiome increased the starch utilization rate in the upper-layer fermented grains by 23.6%, the content of ethanol in the crude Baijiu by 33.3%, and the content of ester flavor substances by 31.4%. At the same time, the functional microbiome significantly increased the relative abundance of Lactobacillus, Limosilactobacillus, Pichia, and Thermoascus while decreasing the relative abundance of Bacillus, Kroppenstedtia, and Aspergillus in the fermented grains. The changes in the relative abundance of these microbial genera led to significant differences in the content of 13 volatile compounds such as caproic acid, caprylic acid, ethyl caproate, and ethyl acetate in crude Baijiu. Spearman correlation analysis indicated that moisture, reducing sugar content, and acidity had significant positive correlations with the main microbial genera and were important driving factors in the fermentation process of fermented grains. Analysis indicated that the functional enzymes and their abundance of the microbial community in the fermented grains showed significant differences at different fermentation stages. It suggested that the microbial community changes in the fermented grains were the main cause of metabolic differences at different fermentation stages. [Conclusion] This study systematically investigated the effects of functional microbiome disturbance on the physical and chemical properties of the upper-layer fermented grains of Nongxiangxing Baijiu, the succession of the microbial community, and the synthesis of volatile flavor substances during the fermentation process, providing a reference for optimizing the brewing process of Nongxiangxing Baijiu through enhancement with functional microbiomes.