Abstract: To investigate the quality variation of tobacco stems of different shapes during a four-stage controlled atmosphere aging process, the bar-shaped and flake-shaped redried stems of Fujian C tobacco stem and Yunnan B tobacco stem were stored for different periods by adjusting the oxygen concentration in the stem storage environment to 21.0%, < 2.0%, 6.0%-10.0% and < 2.0% through the four-stage controlled atmosphere aging technology, and the quality differences between the stems of different shapes were compared. The bacteria 16S rDNA on the surface of tobacco stems during the aging process was analyzed by high-throughput sequencing on the Illumina MiSeq sequencing platform. The changes in moisture content and color of tobacco stems of different shapes during the aging process were tracked, and the sensory quality of cut stems made of aged stems was evaluated. The results showed that: 1)During the aging process, the moisture content and color of flake-shaped stems were more stable, and their color difference value and color deepening rate changed more slowly than those of bar-shaped stems. 2)During the four-stage controlled atmosphere aging, the dominant bacterial phylum on stems of both shapes was Proteobacteria, and the shared dominant bacterial genus of Yunnan B stems and Fujian C stems were Streptomyces, Methylbacillus, Pseudomonas and Sphingomonas. The average OTU number, Chao value, ACE value and bacterial community abundance of flake-shaped stems were higher than those of bar-shaped stems after aging for 6-18 months. 3) The amounts of three dominant aroma-producing bacterial genera, Pseudomonas, Sphingomonas and Bacillas, of flake-shaped stems were higher than those of bar-shaped stems during aging, which was conducive to the improvement of stem quality. 4)After aging, the cut stems made of the flake-shaped stems had less offensive odor, irritation and oral cavity residue than those made of the bar-shaped stems.