Abstract: Aquaculture has rapidly expanded to meet the growing global demand for sea food, but the discharge of nutrient-rich effluent poses significant environment challenges. Therefore, this study explores an efficient and sustainable ecological treatment technology, the integrated ecological purification system, to improve aquaculture effluent quality and support the industry’s long-term ecological balance. In order to understand the purification effect of the integrated ecological purification system on the aquaculture tail water of Litopenaeus vannaiensis continuous freshwater pond, the water quality index of each unit in the system was monitored for two consecutive years. High-throughput sequencing technology and bioinformatics analysis were employed to analyze the microbial community structures in each unit. Correlation analysis and random forest regression model were utilized to assess the relationship between dominant microorganisms and water quality factors. The results indicated that, according to the requirements of Shanghai Municipal Aquaculture Tail Water Standard (DB31/1405-2023), the main pollutants exceeding the standard in the aquaculture effluent were TSS and TN, with exceedance rates of 36.84% and 5.26%, respectively. After treatment in each unit of the system, significant reductions (P<0.05) were observed in the concentrations of TSS, TN, TP, COD_Mn, and TAN, resulting in effluent water quality meeting the standards. The microbial richness increased along the treatment units (P>0.05), with Proteobacteria, Actinobacteriota, and Cyanobacteria being the dominant phyla. The top five dominant bacteria genera explained 51.50%, 23.42% and 18.44% of the variation in NO₃-N, TN and TAN concentrations, respectively. The hgcI_clade was the most dominant bacterium, whose abundance gradually increased along the unit, and exhibited a significant negative correlation with TN and NO_x (P<0.05). Overall, the comprehensive ecological purification system significantly improved the water quality of aquaculture effluent. Different treatment units exhibited varying effects on improving different water quality indicators in the effluent. Microbial communities capable of promoting nutrient metabolism gradually became dominant along the treatment units, significantly influencing the removal of nitrogen pollutants from the effluent. This study provides valuable insights for the practical application and further optimization of multi-level aquaculture effluent treatment systems.