Understanding the pollution status and phytoplankton community structure characteristics of discharge tail water in container recirculating aquaculture system is helpful to improve the efficiency of water quality management and increase aquaculture benefits. In this study, water quality monitoring and phytoplankton sampling were carried out at outlet site A and inlet site B of the system. The difference analysis was used to compare the water quality and phytoplankton community structure between the site A and B. Redundancy analysis (RDA ) was used to analyze the correlation between phytoplankton and environmental factors and identify the main environmental factors affecting phytoplankton community structure. The results showed that the main pollutants were suspended solids (SS) and total nitrogen (TN), the pollutant concentration at site A higher than at site B, and the total pollution index was the highest in May. The removal rate of Ammonia nitrogen (NH4+-N) and SS in the purification area was higher than another pollutant. In addition, 98 species of phytoplankton were detected in the system, including 76 species at site A and 81species at site B, the average phytoplankton density, biomass, Shannon-Wiener diversity index and Margalef richness index were 12.25×106cell/L and 11.67×106cell/L, 26.69mg/L and 34.23mg/L, 1.87 and 1.93, 0.63 and 0.64 in the site A and B, respectively. SS was an environmental factor that significantly affected the phytoplankton community structure at site A, and NH4+-N, TN, total phosphorus (TP) and SS were environmental factors that significantly affected the phytoplankton community structure at site B. This research demonstrates that physical filtration and ecological purification can effectively reduce pollutant concentration and improve phytoplankton biodiversity in container recirculating aquaculture tail water.