Microorganisms play an important role in cigar tobacco leaves (CTLs) production, while the impact of varieties and origins on microorganisms and thereby on aroma profiles were rarely reported. In this study, the aroma profiles of wrapper and filler CTLs from three varieties, respectively, and filler CTLs from four origins were analyzed, and the bacterial and fungal communities of these CTLs and their correlation with aroma constituents were explored. The results showed that ketones and nitrogen heterocycles were dominant in wrapper and filler CTLs of different varieties and filler CTLs from different origins, their proportions in different CTLs were 22.34-58.28% and 19.45-53.62%, respectively. There were significant differences in the varieties and contents of aroma constituents in CTLs of different varieties and origins, which showed obvious variety and origin specificity. For example, the contents of aldehydes (92.24 mu g/kg), ketones (1553.00 mu g/kg), and alkenes (227.14 mu g/kg) in the wrapper variety of AQ2 increased significantly, the contents of ketones (2027.21 mu g/kg), alkenes (219.98 mu g/kg), and total aroma constituents (4262.60 mu g/kg) in the filler variety of QDQX2 increased, and the contents of ketones, nitrogen heterocycles, alkenes, and total aroma constituents in the origin of FXQX1 increased, which increased by 0.29-0.84, 0.44-0.96, 0.22-7.19, and 0.34-0.65 times. Besides, the microbial community diversity and structure were significantly affected by varieties and origins. There were obvious differences in the alpha- and beta-diversity of microbial communities in different varieties and origins of CTLs. Varieties have little effect on the bacterial communities of wrapper and filler CTLs, and only the abundances of the dominant Corynebacterium (45.78-55.34% of wrapper and 29.97-60.90% of filler) and Staphylococcus (15.16-34.60% of wrapper and 22.12-46.70% of filler) were different, but there were significant differences in the composition and abundance of the fungal community. Different from the influence of varieties, the composition and abundance of bacterial communities were significantly changed by the origins, while only the abundances of the dominant Alternaria (6.45-46.73%), Aspergillus (5.72-32.24%), Wallemia (11.80-24.84%), and Cladosporium (1.12-10.89%) in the fungal community were different. Correlation analyses showed that different bacterial and fungal communities synergistically contributed to the formation of aroma profiles of CTLs, and the microbial communities contributing to the formation of aroma profiles were obviously different among wrapper and filler varieties and filler origins.