The filamentous fungus Aspergillus oryzae is widely utilized as starter culture in soy sauce koji fermentation with a long and safe history. Equipped with numerous hydrolytic enzymes, A. oryzae can extensively hydrolyze proteins and complex polysaccharides, contributing to subsequent fermentation and flavor formation. Therefore, good koji, serving as a reserve of enzymes and fermentative agents, can be a premise of high-quality soy sauce production. However, both the molecular mechanisms of A. oryzae metabolism in koji-making process and the microbial community highly relevant to koji quality remain partially understood.In order to understand the molecular basis for koji fermentation performance and the mechanisms behind, an industrial strain RD2 and a strain with decreased fermentation performance TS2 were compared through integrated genomics and transcriptomics. With intact and enhanced hydrolytic enzyme production and flavor precursor formation under the regulation of conidiation and fermentation conditions, RD2 showed a complete expression profile necessary to maintain desirable fermentation performance. On the contrary, genome variants of TS2 might directly impair its koji fermentation performance. A growth advantage due to the enriched central carbon metabolism and amino acid catabolism in TS2 also intrinsically hindered its enzyme production and flavor formation, suggesting a conflicting relationship between mycelium growth and fermentation performance.By profiling the microbial community via amplicon sequencing, the taxonomy diversity and succession pattern of microbial community within koji fermentation were deciphered. Bacterial community was dominated by Enterococcus, Bacillus, succeeded by the family of Enterobacteriaceae; and the predominance of A. oryzae in fungal community was observed during the whole koji-making process. Results also demonstrated that different dynamic bacterial succession between koji fermentation initiated by RD2 and TS2 could coordinate with the metabolism A. oryzae, which drives the production of koji with different quality. The patterns and processes of community assemblies in RD2 presented a microbial community model for desirable koji fermentation.Through integrated omics, this study deepened the understanding of A. oryzae metabolism and related regulation with a list of potential molecular markers identified, which could provide insight into targeted strain maintenance and improvement for better koji fermentation. Also, investigating the microbial consortia from the key fermentative agent and other microorganisms provided a comprehensive knowledge of the microbial ecosystem within soy sauce koji fermentation, enlightening perspectives for effective process control and quality management.