Abstract: To explore the effects of fermentation time on key chemical contents and structure of foliar and internal microbial communities in cigar tobacco leaves, continuous flow analysis was performed alongside metagenomics, 16S rRNA and ITS sequencing technologies. The following parameters were analyzed: key chemical substance contents (mass fractions), the diversity and structure of foliar and internal microbial communities, the symbiotic network among microbial communities. the KEGG functional enrichment of microbial genes, and the correlation between the chemical substance contents and the relative abundance of microorganisms in cigar tobacco leaves fermented for 0-65 days. The results showed that compared to cigar tobacco leaves fermented for 0 days, the chlorine content in the cigar tobacco leaves fermented for 45 days increased significantly (P < 0.05), while the total nitrogen and nicotine contents decreased significantly. There were no significant differences (P > 0.05) in the total sugar, chlorine, potassium, and nicotine contents in the cigar tobacco leaves fermented for 65 days compared with those fermented for 45 days. During the fermentation period from 0 to 65 days, the diversity indexes (Shannon, Simpson, and ACE) of foliar bacterial and fungal communities first increased and then decreased. Compared to 0 days of fermentation, the diversity of the internal bacterial communities increased after 65 days, while the diversity of the fungal communities decreased. After fermentation for 0, 10, 25, 45 and 65 days, the dominant bacterial genera shared by both the surface and inside cigar tobacco leaves were Sphingomonas, Methylobacterium, Pseudomonas, and Aureimonas, while Aspergillus and Penicillium were the shared dominant fungal. The symbiotic networks within microbial communities revealed that foliar microorganisms exhibited a more complex symbiotic structure than those found internally. Additionally, bacterial symbiotic networks tended to be more intricate than fungal ones. The genes of foliar and internal microbes were co-enriched in 167 metabolic pathways, including carbohydrate metabolism, while the internal microbes were specifically enriched in pathways related to color change and aroma formation, such as terpenoid, piperidine, and pyridine alkaloid biosynthesis. The relative abundance of Staphylococcus, a bacterium found on the surface of fermented cigar tobacco leaves, was extremely significantly negatively correlated (P < 0.001) with total nitrogen content. The relative abundance of Sampaiozyma, a fungus found inside tobacco leaves, was extremely significantly positively correlated with total nitrogen and nicotine contents, and extremely significantly negatively correlated with chlorine and potassium contents.