Abstract: The in-pond raceway system (IPRS) based on intensive production of ponds is an emerging aquaculture model. In order to further understand the ecological structure dynamics of this system's water body circulation process and to reveal the change characteristics of water quality in purification area, we studied the spatial variability of phytoplankton community structure and the relationship between the phytoplankton community structure changes and the environmental factors by Redundancy Analysis (RDA) during the growing season in IPRS of grass carp (Ctenopharyngodon idella). The system identified 99 species of phytoplankton in seven phyla, mainly including Cyanophyta, Chlorophyte, Bacillariophyta, Euglenophyta, Cryptophyta, Pyrrophyta and Chrysophyta. Chlorophyta had the largest number of species (54 species), followed by Cyanophyta (18 species). In this system, the phytoplankton community structure in different areas was different. The density and biomass of phytoplankton in the middle of the purification area were the highest, and those of Cyanophyta in the purification area were higer than that in the culture area. The relative density of Cyanophyta in different areas was much higher than those of Chlorophyta and Bacillariophyta. From the front to the back of the purification zone, the relative density of Cyanophyta gradually increased, while those of Chlorophyta and Bacillariophyta gradually decreased. The results of RDA show that the main environmental factors that affect the changes in the phytoplankton community structure in the system are temperature, nitrogen and phosphorus nutrients.