To investigate the differences in gut bacterial community of Parabramis pekinensis at different growth stages, we collected wild P. pekinensis from the Jingjiang region of the Yangtze River, and detected the intestinal microflora structure using high-throughput sequencing technology. Results show that during stage I the dominant bacteria were Proteobacteria, Actinobacteria, and Firmicutes. During stage II, the proportion of Proteobacteria and Actinobacteria decreased, while the proportion of Firmicutes and Fusobacteria increased, especially Clostridium and Cetobacteria increased significantly. During stage III, Cetobacterium had a dominant position, while the proportion of Firmicutes decreased slightly. In stage IV, the male and female fish showed obvious differences. In the female gut, the proportion of Proteobacteria increased to the first place, while Fusobacteria decreased to the second place. In the male fish, the proportion of Fusobacteria dropped to the fifth, especially that of Cetobacterium decreased significantly, and that of Verrucomicrobia increased. In stage V, the proportion of Fusobacteria increased again to the first place, while Proteobacteria did not decrease significantly in the female gut. The gut bacterial community in males changed into a structure similar to stage I. In stage VI, the gut bacterial community in both females and males changed into a structure similar to stage I. There were significant differences in the intestinal microflora structure of P. pekinensis at different gonad development stages and sexes. To some extent, the changes in intestinal microflora structure reflect the changes in the nutritional requirements of P. pekinensis.