Compared with the traditional aquaculture system, three-dimensional cultivation is a potential sustainable cultural pattern that integrates aquaculture with hydroponics in which nitrogen-rich effluent from the fish production is utilized for plant growth. Environmental microbiota plays an important role in the intestinal microbiota of aquatic animals. The association among water, sediment and obscure pufferfish (Takifugu obscurus) intestine under two cultivation patterns should be investigated to reveal the microbiota differences. The aim of the study was to understand the bacterial community structure in different cultural patterns of Takifugu obscurus. Here we compared the microbial community structure with composition variation of water, sediment and the intestine of T. obscures in different cultural patterns to explore the relationship among them. The aim of this study is to provide a reference for the further study of microbiota in the three-dimensional cultivation pattern. Illumina MiSeq high-throughput sequencing method was used to sequence and analyze the two high-variation regions (V3-V4) of 16S rRNA gene of microbia of the water, sediment and intestine of T. obscurus in two cultural patterns (the traditional aquaculture and three-dimensional cultivation). The interactions between water microbia and water environment were analyzed by redundancy analysis (RDA). The interactions between intestine microbial and water environment were analyzed by canonical correlation analysis (CCA). The richness and diversity of the bacterial community of water, sediment and intestine of T. obscurus under three-dimensional cultivation patterns were higher than that in the traditional cultural pattern. The bacterial community structure of water and sediment under three-dimensional cultivation patterns was similar to that in the traditional cultural pattern. Actinomycetes (36.19%), Proteobacteria (26.38%), Cyanobacteria (12.23%), and Bacteroidetes (12.06%) were the dominant phyla in water. Proteobacteria (50.73%) and Bacteroidetes (12.48%) were the dominant phyla in sediment. The dominant genus was Rhodococcu (88.23%) in the intestine in the traditional cultural pattern. However, Staphylococcus (28.93%), Arcobacter(25.36%), norank_f_norank_o_Chloroplast(13.31%), Elizabethkingia (8.56%) and Mycoplasma (5.32%) were the dominant genera in the intestine in three-dimensional cultivation pattern. The results of correlation analysis of environmental factors showed that pH had a significant effect on the water bacterial community. The dominant genus Rhodococcus in water were positively correlated with total suspended solid (TSS), total phosphorus (TP), total nitrogen (TN), pH and nitrate. Total ammonia nitrogen (TAN) had a great influence on the intestine bacterial community of T. obscurus. Rhodococcus and Arcobacter as the dominant bacteria in the intestine were in positive correlation with TSS and TP. Acinetobacter and Mycoplasma were in positive correlation with TAN, nitrite and nitrate. Weissella and Staphylococcus were in negative correlation with TSS, COD, TP, TN, nitrate, nitrite and TAN. The research showed that the use of three-dimensional cultivation pattern could improve the diversity of bacteria in the aquacultural ecosystem, reduce the risk of disease outbreak, inhibit the growth of Cyanobacteria, and reduce the oxidative stress damage to aquaculture objects. Furthermore, the cultural patterns could have a certain effect on water and T. obscurus intestine bacterial community by changing nitrogen and phosphorus concentration in the water．