The purpose of this study was to analyze and compare the effects of the flow-through system (FTS) and re-circulating aquaculture systems (RAS) on operational stability and bacterial succession in shrimp farming systems. In this study, the concentrations of ammonia nitrogen, nitrite and COD in rearing water were detected from the above two systems in Yingkou. The total number of Vibrios and bacteria were also measured. Meanwhile, Illumina Hiseq high-throughput sequencing technology was used to amplify and sequence the bacterial 16SrDNA V4 region in the pond and circulating water system on the 1st, 50th and 100th day of culture. In the beginning, the concentrations of ammonia and COD in FTS and RAS were low. With the increase of aquaculture time, the concentrations of ammonia, nitrite and COD in two types of systems increased. The concentrations of ammonia nitrogen, nitrite and COD in FTS were significantly higher than those in RAS. With the progression of farming, the total number of Vibrio and bacteria increased continuously in both systems, of which FTS has a significant higher abundance of Vibrio spp. and bacteria than those in RAS (P < 0.05), indicating that the sequencing depth of the sample is large enough and the number of OTUs is close to the actual number. Then the gene sequences were clustered by the Operational Taxonomic Unit (OTU), and the bacterial community composition was analyzed based on OTU. The phylum level analysis showed that Proteobacteria and Bacteroidetes were the dominant bacteria in both systems. At the genus level, Vibrio, Rhodobacteraceae and Alteromonas were the main genera in FTS, while the core microbiome in RAS consisted of Rhodobacteraceae, Alteromonas and, Flavobacterium. The results of α diversity showed that the diversity of the bacterial community in RAS was higher than that of FTS, whereas the mean value of Chao1 index in the RAS was also higher than that of FTS (1136.18 vs 1050.82). Finally, a total of 93 strains were obtained in the two modes, of which Vibrio spp. was the main species in FTS, accounting for 61 % of all strains, followed by Enterobacter, accounting for 12 %. In contrast, Vibrio spp. only took up 9 % in RAS. In conclusion, the bacterial diversity and its successional effects of Penaeus vannamei in RAS were more stable than those in the FTS, highlighting the advantages of RAS in maintaining the stability of the aquaculture system and bacterial community.