To study the effects of different fertilization modes on the water bacteria in rice-crayfish co-culture paddy field, Illumina high-throughput sequencing technology was used to detect the bacteria in the water body applying three fertilization modes:chemical fertilizer (CF), organic fertilizer (OF) and organic fertilizer added decomposed chicken manure (OM). The results showed that Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Firmicutes were the main phyla in all treatments. The main dominant genera were Sporichthyaceae hgcl_clade, Limnohabitans, Polynucleobacter, Alpinimonas, Comamonadacea, Hydrogenophaga. In the three models, the bacterial abundance of the OF group was significantly higher than that of the CF group and OM group, and the diversity of bacterial species of OF group was significantly higher than that of the OM group, and there was no significant difference between OF and CF groups. It indicated that in the mode of organic fertilizer application, water microorganisms had better diversity and its ecosystem was more stable. Although the OM treatment reduced the species diversity of bacteria in water, it also can greatly reduced the abundance of Cyanobacteria. Although the species diversity of bacteria in water was reduced under OM treatment, it also greatly reduced the abundance of Cyanobacteria compared to other treatments. The results of cluster analysis showed that the similarity of bacterial community in water was higher between the OF group and OM group. According to the RDA analysis, the dissolved oxygen, total nitrogen, pH and total phosphorus were the most important environmental factors affecting water bacteria. The aim is to understand the effects of different fertilization treatments on the ecological environment of paddy fields and provide a theoretical basis for the optimization of paddy field comprehensive fertility model.