Abstract: In order to clarify the purification effect of the treatment system for eel aquaculture tail water and the changes in the composition and structure of microorganisms in different units of water, the water quality of each unit was detected and the microbial community composition in the water at different treatment stages was analyzed by 16S rRNA high-throughput sequencing technology. The results showed that:After the purification treatment, the total phosphorus content and ammonia nitrogen concentration of the water decreased, and the pH of the water increased; the purified water body and river water samples had 6 same dominant bacteria genera, among which Novosphingobium, Limnohabitans, and Sediminibacterium were the top 10 bacteria genera in the samples. The chemical treatment of phosphorus removal and purification treatment could greatly change the microbial community structure of the aquaculture tail water, while the biological treatment could make the microbial community structure of the water body closer to the natural water body. The study revealed the water quality conditions of water body and the dynamic changes of the microbial composition in water body at different stages of tail water treatment, indicating that the ecological units in the tail water treatment system could effectively improve the micro-ecological balance in the aquaculture tail water environment.