Clear-flavored, intermediate-flavored, and strongly flavored tobacco leaves respectively from Yuxi of Yunnan, Chenzhou of Hunan, and Zunyi of Guizhou, which had been mellowed for 1 year, were selected to test the main chemical composition of the tobacco leaves. The similarity test was used to analyze the differential species of the microbial community, the molecular ecological network was constructed based on the random matrix theory, and the correlation analysis was carried out by Mantel test. The results showed that there were significant differences in the structure of microbial communities among the three flavored tobacco leaves and the highest ɑ diversity index of bacterial and fungal communities were found in the strongly flavored tobacco leaves. Pseudomonas, Enterobacter, and Sphingomonas were the key bacterial groups and Alternaria, Rhizopus, and Sampaiozyma were the key fungi that were enriched in the three flavored tobacco leaves. The microbial ecological network of strong flavor tobacco leaves was the largest among the three flavored tobacco leaves, and the network was complex and relatively stable. Total sugar and reducing sugar content significantly affected the diversity and structure of the microbial community of tobacco leaves. The key microbial taxa of clear and intermediate flavor tobaccos were significantly positively correlated with the total sugar and reducing sugar content, whereas the key microbial taxa of strong flavor tobaccos were significantly negatively correlated with the total sugar and reducing sugar content.