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Grass carp (Ctenopharyngodon idellus) is the most productive freshwater fish in China, but its traditional aquaculture model still has problems, such as poor water quality and frequent diseases. We have taken monoculture and 80:20 polyculture grass carp ponds as the research object and used EwE software to build the Ecopath model of two ponds. We analyzed and compared the characteristics of ecological structure and energy flow in two ponds. The result showed the highest effective trophic level in the polyculture pond that was higher than that in the monoculture pond, and fish in polyculture had higher EE values which showed the production of fish in polyculture contributed more to the energy conversion efficiency of the ecosystem. Flows into detritus were the largest component of TST both in the two ponds, which accounted for 49.34% and 50.37%. And the average transfer efficiency in monoculture was 13.07%, while that in polyculture was 15.6%. The ascendency/total development capacity (A/TDC) and overhead/total development capacity (O/TDC) were 0.35 and 0.65 both in the two ponds, respectively, which indicated that both systems had a strong anti-perturbation ability, but the stability could be improved. Finn's cycling index (FCI) in polyculture was higher and showed that the polyculture pond was more mature and stable. Unused energy of functional groups will flow to detritus, and that in the monoculture pond was higher, the energy of C. idellus that flowed to detritus in monoculture was 48.17% higher than that in polyculture; unused energy of bacteria and phytoplankton were also high. The result showed that polyculture could improve energy utilization, increase transfer efficiency, and raise the stability of the ecosystem. Grass carp ponds still need to be improved in the aspects of mixed species and energy consumption. It is necessary to improve the ecological and economic benefits of grass carp ponds by optimizing the aquaculture structure and adjusting the aquaculture proportion. [ABSTRACT FROM AUTHOR]