In order to know more about the correlations between the stocking densities and the community structure of zooplankton in aquaculture pond of Gymnocypris przewalskii, the community structure of zooplankton, the water quality index and the growth of Gymnocypris przewalskii were determined through continuous sampling survey of Gymnocypris przewalskii ponds with different stocking densities. The impact of stocking densities of Gymnocypris przewalskii on the community structure of zooplankton in ponds was discussed and analyzed. The results showed that 39 species of zooplankton, mainly rotifers, were determined during the experiment, which accounted for 61.5% of the total zooplankton species. The density, biomass and diversity index of zooplankton decreased with the increase of culture time in medium and high density conditions. The study showed that high density breeding had a great impact on the community structure of zooplankton, and the high feeding pressure on zooplankton caused by medium and high density breeding fish fry restricted the growth of zooplankton. The zooplankton species decreased and tended to be miniaturized, which was not conducive to the stability of the aquaculture water environment.