Background <p>Fermentation, a fundamental process in the production of cigar tobacco leaves, substantially influences the improvement of tobacco leaf quality. The initial water content is a crucial factor that regulates the fermentation process. This research systematically analyzed the dynamics of volatile aroma components, microbial community structure, and differential metabolites during the fermentation of cigar tobacco under three initial water content conditions (H1, H2, and H3).</p> Results <p>For three different initial water contents of cigar tobacco leaves, GC–MS analysis examined changes in key aroma compounds during the fermentation; Metagenomic analysis revealed differences in the microbial community composition of tobacco leaves, identifying characteristic microorganisms at the species level. Correlation analysis further elucidated the relationship between these characteristic microorganisms and flavor compounds; Untargeted metabolomics identified differential metabolites and their corresponding metabolic pathways during fermentation.</p> Conclusion <p>The research findings provide theoretical guidance for further optimizing the fermentation process and enhancing the quality of cigar tobacco leaves.</p> Graphical Abstract <p></p>