As the foundation of material circulation and energy flow, microbes play an important role in an aquaculture environment. Consequently, to understand and predict the response of ecosystems to environmental changes, it is necessary to explore the structure and constructive mechanism of microbial communities in aquaculture ponds. Since their introduction from the US in 1984, both the cultivation areas and the production of channel catfish have increased dramatically in China. Along with the US, China has become a major producer and consumer of channel catfish. This study characterized the structure of microbial communities in sediment samples from a channel catfish pond. High-throughput sequencing (Illumina MiSeq) of the V3-V4 hypervariable region in the 16S rRNA gene was used to investigate microbiome structural characteristics. The results showed that the bacterial community structure presented a seasonal change. Samples in winter and spring were more similar than others. The dominant phyla in sediment samples were Proteobacteria, Chloroflexi, Bacteroidetes, Firmicutes and Acidobacteria, which were apparently different from that in the water body of the channel catfish pond. No significant difference of α-diversity was detected between the four seasons. Among the measured environmental variables, water transparency (SD) and total dissolved solids (TDS) were observed as the primary drivers for bacterial communities, which had a significant correlation with the bacterial community structure (<0.05). These results might provide basic references for understanding and managing the bacterial community composition in channel catfish ponds.