[Objective] This study examined the characteristics of the microbial communities and their associations with chemical components in aged tobacco leaves from different production areas in Yunnan Province, aiming to provide a theoretical foundation for the targeted exploitation of tobacco microbial resources and quality improvement of tobacco. [Methods] A systematic approach integrating metagenomic sequencing, GC/LC-MS, and Spearman’s correlation analysis was employed to investigate the microbial communities, chemical components, and their correlations of aged tobacco leaf samples collected from Dali, Wenshan, Honghe, Luoping, Pu’er, Zhaotong, and Lincang. [Results] The dominant bacterial phylum was Pseudomonadota in aged tobacco leaf samples. The dominant bacterial genera varied among different production areas. Specifically, Salinivibrio was identified as the core genus in the samples from Wenshan, while Methylobacterium and Sphingomonas exhibited significant enrichment in the samples from Luoping. For fungal communities, Ascomycota and Mucoromycota were the predominant phyla, and dominant fungal genera showed negligible variations. Alpha diversity analysis revealed the highest microbial richness and diversity in the samples from Lincang and the lowest in the samples from Wenshan. KEGG analysis revealed that metabolic pathways exhibited high relative abundance across samples from all regions, whereas environmental information processing pathways were more abundant in the samples from Wenshan. CAZy analysis showed that genes annotated as glycoside hydrolases (GHs) and glycosyl transferases (GTs) were the most prevalent, with both generally exhibiting lower abundance in the samples from Wenshan. Chemical profiling revealed that reducing sugar, total sugar and other conventional components were more concentrated in the samples from Dali, whereas total sugar-to-nicotine ratio and potassium-to-chloride ratio were elevated in the samples from Pu’er. Additionally, neutral aroma compounds, including benzyl alcohol, had significantly higher levels in the samples from Wenshan, while polyphenols such as anthocyanins exhibited markedly higher concentrations in the samples from Luoping. Correlation analysis further disclosed that Microbacterium had a significantly positive correlation with total nitrogen, while Aureobasidium showed a significantly negative correlation with total nitrogen. Leucosporidium exhibited significantly positive correlations with potassium ions and potassium-to-chloride ratio. Salinivibrio had significantly positive correlations with multiple neutral aroma components. In contrast, Methylobacterium and Friedmanniomyces showed significantly negative correlations with the majority of neutral aroma components. Additionally, Methylobacterium, Sphingomonas, Friedmanniomyces, and Metschnikowia had significantly positive correlations with multiple polyphenols. [Conclusion] Microbial communities and chemical components of aged tobacco leaves exhibited marked differences across different production areas in Yunnan. Notably, dominant genera are strongly correlated with aroma compounds, which lays a theoretical basis for targeted screening of functional microbes and the development of biotechnologies to improve tobacco quality.