Microbial communities in the intestine of Macrobrachium rosenbergii under six cultural patterns were evaluated by high-throughput pyrosequencing technology. The interactions between microbial and water environment were also analyzed by RDA (Redundancy analysis). The cultural patterns included prawn monoculture group (MP), prawn with aquatic plant (Lemna minor) group (PP), prawn with silver carp (Hypophthalmichthys molitrix) group (PF), prawn with mussel (Anodonta woodiana) and H. molitrix group (PMF), prawn with mussel and aquatic plant group (PMP), prawn with A. woodiana, L. minor and H. molitrix group (PMPF). Four replicates of each treatment were set up. After 64 days of culturing, the microbial communities and physico-chemical factors were assessed. There were significant differences in turbidity, soluble phosphorus (PO₄-P), total nitrogen (TN) and chlorophyll-a (Chl.a) among groups, and PO₄-P concentration in MP group was significantly higher than those in other groups (P<0.05). Shannon diversity index of intestinal bacteria was the highest in the MP group (4.08), and the lowest in the PMF group (1.27). Proteobacteria, Tenericute and Firmicutes were the major dominant phyla in intestine of M. rosenbergii in the six groups. The major dominant genus was different in six groups, which was Aeromonas in MP, PMP and PMPF groups, and Citrobacter in PP group, and Candidatus and Hepatoplasma in PF and PMF groups. The interaction analysis between intestinal bacteria and environmental factors showed that total phosphorus (TP) had significant effects on the intestinal bacterial community of M. rosenbergii (P<0.05), Adaptation of microorganisms to the environment factors was different, and the abundance of Aeromonas enteropelogenes, beneficial Enterococcus and Lactococcus garvieae were positive correlation with NO₃-N and TN. Rhodobacter and Pseudomonas vranovensis were positive correlation with TP. Conclusively, cultural patterns can affect the intestinal bacterial community of M. rosenbergii by affecting the nutrient concentration in the water, especially nitrogen and phosphorus.