Abstract: In the polyculture ponds dominated with grass carp (Ctenopharyngodon idellus), the physico-chemical index and community structure of plankton and microbial in pond water with or without fermented organic fertilizer were measured to analyze the effects of fermented organic fertilizer on water environment of polyculture ponds. The results showed that the diversity and biomass of zooplankton, phytoplankton and bacteria increased significantly in the fermented organic fertilizer ponds. During the experiment, monthly average biomass of phytoplankton, zooplankton, and the average abundance of microbial were (68.21±25.13) mg/L, (9.83±5.74) mg/L and (6.53±2.13)×10⁶ ind./mL, which were 2.78, 4.35 and 1.29 times of those in the control ponds, respectively. Furthermore, the proliferations of beneficial bacteria were significantly promoted by using fermented organic fertilizer. In later stage, the relative proportions of Lactobacillus, Bacillus and Arthrobacter were (0.61±0.17)%, (0.89±0.29)% and (0.04±0.0082)%, which were 3, 3 and 4 times of those in the control ponds, respectively. In rapid accumulation season of \rmNH_4^ + -N and \rmNO_2^ – -N, the concentrations of \rmNH_4^ + -N and \rmNO_2^ – -N were significant lower than those of control ponds (P<0.05), which indicated that the fermented organic fertilizer had a remarkable effect on stabilizing the concentration of \rmNH_4^ + -N and \rmNO_2^ – -N. Moreover, the oxygenation improved significantly by fermented organic fertilizer, while the pH value, TN, TP, \rmNO_3^ – -N, and \rmPO_4^3 – -P concentration were not significantly different (P>0.05) from those of the control ponds. All of the results mentioned above indicated that the effectiveness of fermented organic fertilizer was prominent and it could significantly improve the water environment of polyculture ponds.