Abstract: Controlled atmosphere aging (CAA) is a method of tobacco strips aging. Microorganisms, especially bacteria, play an important role in smoking quality of tobacco during the aging process. In order to study the alteration of bacterial community structure in tobacco strips during the process of CAA, the diversity of bacterial 16S rDNA sequences were carried out. 36 samples were compared by using Illumina MiSeq sequencing platform in three stages including the mildew and insect control stage(S1), the aging stage (S2) and the quality guarantee stage(S3). The results showed that the species richness and diversity of bacteria in tobacco strips increased from S1 to S3. The dominant populations of tobacco strips in S1 were Sphingomonas, Pseudomonas and Methylobacterium, with a proportion of which gradually decreased during the whole process of CAA. The dominant populations in S2 were Bacillus, Burkholderia and Sphingomonas, with a proportion of Bacillus and Burkholderia increased first and then decreased in the whole process. The distribution of bacteria population in S3 was more uniform. Nonmetric multidimensional scaling analysis showed that the samples of three aging stages could be distinguished clearly. It was clear that the tobacco strips in CAA process harbored abundant levels of bacteria, and the active microbial groups were different in different aging stages. Sphingomonas, Pseudomonas and Methylbacterium were mainly involved in the early process, while Bacillus and Burkholderia mainly played an important role in the later process.