In order to analysis the soil bacterial structure community in different paddy co-cropping models, high throughput sequencing technique was used to study the diversity of bacterial community, richness and changes of community structure in the surface soil of rice field at panicle setting stage for rice field monoculture, river crab paddy field co-cropping and lobster rice field co-cropping. A total of 46 phyla,112 classes, 210 orders, 370 families,664 genera and 1 227 species of bacteria were detected. The dominant phylum is Proteobacteria, Bacteroidetes,Chloroflexi, Actinobacteria and Acidobacteria. The chao index of crab paddy field and lobster paddy field is higher than that of monoculture rice field. The results of PCoA analysis showed that the composition of soil bacterial community for crab rice field and lobster paddy field was quite different from that of rice field monoculture. The study showed that the ecosystem of rice co-cropping with crab and lobster had richer microbial ecological components.