This experiment was conducted to study the effects of complex probiotics on water quality and microbial community structure in grass carp culture. The results of water quality determination showed that compared with the control group, the concentration of ammonia nitrogen, nitrite nitrogen and total nitrogen in treatment group was lower in the whole experiment, respectively; At 18th d, the concentration of nitrate nitrogen in treatment group was decreased by 54.49% (P<0.05). At 15th d, the concentration of total inorganic nitrogen in treatment group was decreased by 28.75%（P<0.05）. Orthophosphate and total phosphorus was no difference between the two groups. The 454-Pyrosequencing results showed that the composition of bacterial communities was highly variable between control and treatment group, and microbial diversity of treatment was higher than that of contorl. Firmicutes and Proteobacteria was decreased by 91.21% (P<0.01) and 21.75% (P<0.01) respectively. Bacteroidetes, Actinobacteria and Cyanobacteria was increased by 2.88 times (P<0.01), 4.35 times (P<0.01) and 8.48 times (P<0.01) respectively. Among Proteobacteria，Alphaproteobacteria and Betaproteobacteria was elevated by 3.18 times (P<0.01) and 18% respectively, when Gammaproteobacteria was reduced by 78.82% (P<0.01).