In order to study the water quality of offshore scallop culture waters, the distribution of bacterial populations and the response of microbial community diversity to environmental factors, we collected the seawater samples from different stations in the offshore Chlamys scallop culture area of Qingshan Village in Laoshan Bay, Qingdao from May to October 2019. Through the high-throughput sequencing method the differences in the microbial community structure and diversity in different months were analyzed, and the correlation between environmental factors and the microbial community structure was discussed. The results showed that: ①52 phyla and 115 classes were detected in bacterial community structure. It composed of Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria， Firmicutes，etc,among which Proteobacteria was the dominant phylum，mainly including γ-Proteobacteria and a- Proteobacteria. ②In September, the bacterial diversity in the water samples of the aquaculture area increased and the cells number reached the highest level, while the diversity of Vibrio decreased, indicating the possible existence of vibrio disease outbreak. ③The RDA redundancy analysis showed that turbidity (P= 0.027) had a significant impact on the species composition and community structure of the bacteria OUT level in the intensive culture areas. Nitrate (P=0.017) and turbidity (P=0.033) had a significant impact on the species composition and community structure of the OTU level in a sparse culture area. ④The heatmap analysis on the correlation between environmental factors in different regional bacterial phylum levels showed that the aquaculture activities affect the degree of interaction between the bacterial community structure and environmental factors in the coastal waters，thereby increasing the possibility of disease occurrence. The results of this study can provide a theoretical basis for the occurrence of shellfish diseases and the healthy development of coastal ecosystem.