| Microbial community composition plays an important role in aquaculture systems, affecting the nutrition and immune response of aquaculture organisms. In this study, we investigated the microbial community structure and diversity in the water and sediment of Chinese mitten crab ecological breeding ponds in Sheyang, Jiangsu Province, aiming to provide a reference for environmental protection and healthy breeding of the crab. Water and sediment samples (labeled as S7，S8，S9 and N7，N8，N9) were collected from three breeding ponds in the aquatic seedling farm of Sheyang County. The V3–V5 hypervariable region of the 16S rRNA gene from bacteria in water and sediment samples was sequenced using high-throughput sequencing technology and expressed in operational taxonomic units (OTUs) using MOTHUR software. The resulting sequences with less than 97% sequence similarity were clustered using Qiime（v1.7）software and the richness and diversity of the microbial community were evaluated based on the Chaol index and Shannon index. Ponds 7, 8, and 9 displayed, respectively, 8881, 7406 and 8566 OTUs. The microbial community of water sample S7 included 191 genera, 97 families, 58 orders, 29 classes and 16 phyla; for S8, 132 genera, 68 families, 38 orders, 18 classes and 9 phyla; and for S9, 227genera, 111 families, 60 orders, 32 classes and 17 phyla. The microbial community of sediment sample N7 included 572 genera, 352 families, 198 orders, 103 classes and 41 phyla; for N8, 534 genera, 318 families, 203 orders, 103 classes and 42 phyla; and for N9, 578 genera, 323 families, 196 orders, 99 classes and 40 phyla. Proteobacteria was the dominant taxa detected in the water and sediment samples, followed by Bacteroidetes. The abundance and diversity of microbes in the sediment were much higher than in the water. The information provided by this study will be helpful in rearing Chinese mitten crab larvae.