To investigate the differences in the compositon and diversity of bacterial community in the intestine, water and sediment of rice-crab co-culture and crab monoculture models, Illumina sequencing of the V4 hypervariable region 16S rRNA gene revealed extensive changes in bacterial communities. At the phylum level, 7 bacterial phyla were found, including Acidobacteria and Synergistetes in the intestine, Bacteroidetes, Cyanobacteria, Gemmatimonadetes and Armatimonadetes in the water, Planctomycetes in the sediment. At the genus level, there were 14, 18 and 13 bacterial genera in the intestine, water and sediment respectively. No significant differences in the abundance indexes (Chao, ACE) and the diversity indexes (Simpson, Shannon) of the intestinal, water and sediment samples were observed between two production models. Comparative analysis of bacterial groups with significant difference in the water and sediment (Mycobacterium, Rhodobacter, Flavobacterium, Nitrospira, Cyanobacteria, Acidobacteria, Planctomycetes, Tenericutes and Firmicutes)revealed bacterial species that indicate an anaerobic or high nitrite environment was more abundant in the samples of crab monoculture model. The composition of intestinal bacterial community of rice-crab co-culture model was closer to that in wild populations, which also indicated the environment of rice-crab co-culture is healthier than crab monoculture and is beneficial to the growth of Eriocheir sinensis.