ABSTRACT Acetic acid fermentation (AAF) is a vital stage in the production of Shanxi aged vinegar (SAV), during which microbial community succession and metabolic reprogramming jointly determine acidification efficiency and flavor development. However, the system‐level mechanisms linking microbial dynamics to functional metabolism during AAF remain insufficiently understood. In this study, metatranscriptomic analysis was employed combined with KEGG pathway enrichment, CAZy profiling, and global metabolic network visualization to elucidate the functional landscape of AAF across different fermentation stages. The results indicated a pronounced stage‐dependent metabolic shift during AAF. In the early stage, nucleotide biosynthesis, and sugar metabolism pathways were highly active, accompanied by strong expression of CAZy‐related genes, suggesting a growth‐oriented metabolic strategy driven by efficient polysaccharide degradation and carbon assimilation. As fermentation progressed, mainly Acetobacter and Komagataeibacter , became functionally dominant, reinforcing nitrogen metabolism and central carbon metabolism. In the late stage, increasing acid stress induced a transition toward maintenance‐ and stress‐adaptation‐oriented metabolism, characterized by enhanced oxidative phosphorylation, ATP‐dependent proton transport, nitrogen assimilation, and amino acid metabolism. Notably, amino acid metabolism emerged as a key metabolic axis linking stress tolerance and flavor maturation, while a clear functional division of labor between Lactobacillus and Acetobacter was observed, forming a cooperative metabolic network that stabilized fermentation performance. Collectively, this study provides a system‐level view of microbial and metabolic coordination during SAV AAF and offers mechanistic insights into the self‐organizing nature of solid‐state vinegar fermentation.