Abstract: To investigate the community structure and macromolecular substances degradation function of surface microorganisms on different aged cigarette raw materials, the structures of microorganism communities in the samples of flue-cured tobacco stems and strips and oriental tobacco aged for two years were analyzed using metagenomic sequencing technology, and the correlation analysis between the contents of pectin, cellulose, starch, protein and lignin and the community composition of surface microorganisms of the samples were carry out. The results showed that among the three types of aged samples, the contents of starch and protein in aged flue-cured tobacco stems and those of pectin, cellulose, and lignin in aged flue-cured tobacco strips were the lowest. The dominant bacteria in aged flue-cured tobacco stems were Pantoea, Acinetobacter, Klebsiella, and Pseudomonas, those in aged oriental tobacco were Pantoea, Pseudomonas, and Acinetobacter, and those in aged flue-cured tobacco strips were Pantoea, Bacillus, and Terribacillus. Sphingomonas had more genes involved in starch degradation, and its relative abundance was negatively correlated with the starch content in the aged samples. Sphingomonas, Stenotrophomonas, and Klebsiella had more genes involved in protein degradation, and their relative abundances were negatively correlated with the protein content in the aged samples. Bacillus had more genes involved in pectin degradation, and its relative abundance was negatively correlated with the pectin content in the aged samples.