Abstract <p>Microorganisms play a crucial role for metabolism of tobacco during aging, which affects the final quality of tobacco products. Therefore, this study aimed to clarify the microbial community and metabolic profiles of tobacco at different durations of aging. Almost all volatile metabolites of tobacco, such as ethyl hexanoate (M/D), butanoic acid ethyl ester, isoamyl formate, ethyl propanoate, ethyl heptanoate, and benzaldehyde (M/D), decreased with aging. In contrast, non-volatile metabolites (organic acids, terpenoids, and amino acids) of tobacco increased with the aging time. Besides, metabolomics analyses revealed that, after 2&#xa0;years of aging, <i>Macalpinomyces</i>, and <i>Cladosporium</i> increased from 0.08% and 1.4% to 14.28% and 8.53%, respectively. In addition, analysis of the correlation between microbiota, and metabolites indicated that <i>Sphingomonas carotinifaciens</i> is associated with most volatile metabolites (12 types) during tobacco aging, whereas <i>Ustilago trichophora</i>, <i>Moesziomyces aphidis</i>, <i>Alternaria alternata</i>, <i>Naematelia encephala</i>, and <i>Kockovealla imperatae</i> were found to be positively correlated with multiple non-volatile metabolites, including glutaconic acid, arachidonoyl amide, and kopsiloscine. Thus, this study provides novel insights into the diversity of microbes and their role in regulating the metabolites of tobacco during aging.</p> Graphical abstract <p></p>