Abstract: To clarify the influence of microbial communities on the transformation of chemical components and formation of aroma characteristics in flue-cured tobacco, this study utilized Illumina sequencing to analyze the bacterial and fungal community compositions in fresh, intermediate, and strong aroma type of tobacco leaves, along with their correlations with chemical components. The results revealed significant differences in microbial community diversity among the three aroma types. The bacterial Simpson index was significantly lower in intermediate-aroma type leaves than that in fresh- and strong-aroma types, while the fungal ACE, Chao, and Simpson indices were significantly higher in intermediate-aroma type leaves. At the genus level, Enterobacter showed the highest relative abundance in fresh- and strong-aroma type leaves, accounting for 27.97% and 36.4%, respectively. Methylobacterium-Methylorubrum was overwhelmingly dominant in intermediate-aroma type leaves, with a relative abundance of 25.41%. The dominant fungal genera were Aspergillus (fresh-aroma), Sampaiozyma (intermediate-aroma) and Alternaria (strong-aroma), with relative abundance of 40.54%, 39.65%, and 29.00%, respectively. In the microbial network structures of the three aroma type tobacco leaves, strong-aroma type exhibited the highest average clustering coefficient and modularity, suggesting a stable and complex microbial community. Significant enrichment of Enterobacter in fresh- and strong- aroma types, and Alternaria in strong-aroma type showed significant positive correlations with scopoletin, chlorine, reducing sugar and total sugar content, but significant negative correlations with nicotine and chlorogenic acid content. This study elucidates the microbial composition differences among different aroma types of tobacco leaves and their potential roles in shaping tobacco aroma characteristics in flue-cured tobacco.