Using the high-throughput sequencing technology of Miseq, the microbial structure of the intestine and water biofloc of Fenneropenaeus merguiensis at high, medium and low aquaculture densities(700/m3, 300/m3, 100/m3) were analyzed. The results showed that among the shrimp intestinal flora, the high-density group had the highest abundance and diversity, and the abundance increased over the increase of stocking density, while among the biofloc flora, the high-density group had the lowest abundance. The intestinal and biofloc flora samples were mainly composed of Proteobacteria(relative abundant 49.25%~80.33%), Actinobacteria, Bacteroides and Chloroflexi at phylum level, but the abundance was different. At genus level, the composition and proportion of dominant bacteria were significantly different. Clostridium, Spongiibacter, Faecalibacterium, Rhodovulum, and Blautia only exist in intestinal samples, and Coccinimonas only exist in biofloc samples. The relative abundance of Vibrio was relatively large, Vibrio abundance of intestinal sample was the smallest(5.23%) in medium density group and the largest(23.39%) in high density group; the low-density group of biofloc samples was the largest(16.15%), and the medium and high-density samples were both smaller, the abundance was 5.51% and 4.20%, respectively. The abundance of Bacteroides in the intestinal samples decreased with the increase of stocking density, and the abundance was 1.36%, 0.41%, 0.02%, respectively. The abundance difference of Bacteroides in different culture density biofloc samples was not significant. It can be seen that under the bioflocculation mode, the density of culture had a greater influence on bacterial community characterization of biofloc and intestine of Fenneropenaeus merguiensi.