Abstract: In order to explore the seasonal changes of the bacterial community structure and the interaction of environmental factors in Sinonovacula constricta ponds, we used high throughput sequencing technology to examine the bacteria of water, sediment, and viscera. The results showed that microflora structure of water samples in winter was significantly different from that in spring, summer and autumn, while there was no significant difference in bacterial community structure of sediment and viscera in different seasons. There was no significant difference of Shannon diversity index in water across different seasons. The Shannon diversity index of sediment and viscera was the lowest in summer and the highest in winter. At the phylum level, Cyanobacteria, Proteobacteria and Tenericutes were the most predominant bacteria in water, sediment, and viscera, respectively. At the genus level, NS3a_marine_group was predominant in winter water, and Synechococcus in the other three seasons. By contrast, dominant bacteria in sediments were norank_f_Anaerolineacea and Nitrospira, and Mycoplasma and Arcobacter were the most abundant bacterial genera in viscera. Synechococcus had a positive correlation with water temperature, COD, PO₄^--P, NH₄⁺-N, pH, and transparency. The norank_f_Anaerolineacea was positively correlated with water temperature, COD, and TP. Mycoplasma was positively correlated with water temperature, PO₄^--P, NH₄⁺-N, pH, and transparency. Our results suggest that there were significant differences in the composition and diversity of microflora of S. constricta and ponds in different seasons. Bacteria in water was obviously affected by various environmental factors, especially water temperature and the concentrations of nitrogen and phosphorus.