In order to research the change pattern of phytoplankton community structure in pond industrial eco-aquaculture system and explain its ecological mechanism, the experiment was carried out using Megalobrama amblycephala as aquaculture species and setting two stocking density. Shannon-Wiener diversity index and Pielou uniformity index were used to study the phytoplankton community structure in aquaculture area (including Low stocking density aquaculture area and High stocking density aquaculture area), Inlet area, Outlet area, Purification area, Recirculation area, Back area of pond industrial eco-aquaculture system. The results showed that 5 phyla including 92 species have been found, including Chlorophyta 46 species, Cyanophyta 15 species, Euglenophyta 15 species, Bacillariophyta 10 species, Cryptophyta 5 species, Pyrrophyta 1 species. The numbers of phytoplankton species, biodiversity indexes, uniformity indexes, chlorophyta biomass and its proportion accounting for the total phytoplankton followed the order of Inlet area, Purification area, Recirculation area, Back area>Low stocking density aquaculture area >High stocking density aquaculture area>Outlet area. The total biomass of phytoplankton, Cyanophyta and its proportion accounting for the total phytoplankton followed the order of Inlet area, Purification area, Recirculation area, Back area< Low stocking density aquaculture area