Abstract: The quality of cigar tobacco is co-determined by variety characteristics and fermentation-associated microbiota. This study aims to analyze the structure of the phyllosphere microbial community during the fermentation of different cigar tobacco varieties and its correlation with major chemical components. The findings will provide a theoretical basis for elucidating the microbiological mechanism of variety-specific flavor formation. Two high-quality cigar tobacco varieties Qingxue 107 (QX) and Yunxue 6 (YX) were fermented under constant temperature and humidity conditions. High-throughput sequencing of bacterial 16S rRNA and fungal ITS regions, combined with chemical components analysis, was employed to compare phyllosphere microbial communities before and after fermentation between the two varieties and their correlations with chemical indices. Phyllosphere microbial communities differed significantly between the two varieties post-fermentation. QX exhibited significantly elevated Shannon and reduced Simpson indices for both bacterial and fungal communities. Methylobacterium-Methylorubrum, Acinetobacter, and Pseudomonas emerged as dominant bacterial genera, with Sampaiozyma becoming the dominant fungal genus. By contrast, YX exhibited reduced bacterial diversity post-fermentation, with Staphylococcus becoming markedly dominant, followed by Brevundimonas. Fungal communities remained predominantly Aspergillus and Wallemia. Random forest analysis further revealed that Pseudomonas was a characteristic bacterial genus for YX both before and after fermentation, whereas QX possessed more characteristic fungal genera, such as Talaromyces, after fermentation. Co-occurrence network analysis indicated that Staphylococcus and Aspergillus served as shared antagonistic hubs for bacterial and fungal communities in both varieties, respectively. Conversely, Methylobacterium-Methylorubrum and Brevundimonas acted as synergistic hubs in QX and YX, respectively, reflecting variety-specific microbial interaction patterns. Chemical analysis showed that YX had significantly higher contents of potassium, chlorine, reducing sugar, starch, total nitrogen, and protein than QX post-fermentation, whereas its nicotine content was lower. Correlation analysis revealed that reducing sugar content was significantly positively correlated with Acinetobacter but significantly negatively correlated with Staphylococcus. Potassium content showed a significant positive correlation with Brevundimonas, while protein content was positively correlated with Sphingomonas but negatively correlated with Brevundimonas. These findings demonstrate that key microbial communities play crucial functional roles during fermentation, and differences in core microbial hubs drive variety-specific variations in community function and chemical transformation.