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In order to investigate the quality differences of cigar tobacco leaves from Yunnan production areas, microbial community structure, free amino acids and volatile flavor compounds of cigar tobacco leaves produced in Yunnan province were analyzed by high-throughput sequencing and metabolomics. O2PLS analysis and correlation analysis were used to systematically reveal the relationship between microorganisms of origin and tobacco flavor quality, and to identify functional microorganisms and synergistic taxa in tobacco. The results showed that there were differences in the microbial community structure of cigar tobacco leaves produced in Yunnan province, in which the dominant bacteria were mainly Aerococcus, Staphylococcus and Corynebacterium, and the dominant fungi were mainly Aspergillus, Cladosporium and Alternaria. 17 free amino acids were detected, and the overall amino acid content showed that Asp was the highest and Met was the lowest, with higher TAV Asp and Glu contributed more to its flavor presentation. The free amino acid flavor profiles of Lincang Yunxue No. 2 and Pu'er Yunxue No. 2 cigar tobacco leaves was more prominent. A total of 65 volatile flavor compounds were detected, mainly ketones, among which 16 different flavor compounds, including 6-Methyl-5-hepten-2-one, ß-Damascone, Phenylethyl alcohol, Decanal, and Dihydroactinidiolide, played an important role in the formation of its flavor. The overall flavor characteristics of Pu'er No. 2 were more prominent. Sphingomonas, Staphylococcus, Pseudomonas, and Oceanobacillus acted synergistically to contribute to cigar tobacco leaves flavor formation, while the relative abundance of Penicillium was negatively correlated with tobacco quality. [ABSTRACT FROM AUTHOR]