Abstract: The algal-bacterial symbiotic system (ABSS) demonstrates promising potential for treating aquaculture effluent, with the algal-bacterial inoculation ratios and algal species being key factors influencing the system's treatment efficacy. To enhance the purification efficiency of aquaculture effluent, we analyzed the effects of different algal species and inoculation ratios on the ABSS treatment of freshwater aquaculture effluent. Combined with microbial community analysis, the purification mechanism was explored at the microscopic level. The results indicate that the ABSS exhibited optimal purification performance at a ratio of Chlorella: Chlorella: activated sludge=1:1:6. Ammonia nitrogen removal reached 100% within 12 hours, while nitrate nitrogen, nitrite nitrogen, and total nitrogen were nearly completely removed within 72 h. Its comprehensive denitrification effect significantly outperformed all the control groups and other algal-bacterial ratios systems. Microbial community structure analysis reveals that the type of algal species affected the construction of the inter-algal microbial community. Compared with single-algal or single-bacterial systems, the algal-bacterial symbiotic system significantly enriched denitrifying bacterial genera such as Pseudomonas and Bacillus. Functional prediction analysis further indicates that the mixed algal system enhanced metabolic functions related to ammonium oxidation and nitrate reduction, forming a more structurally diverse and functionally complex microbial community, which supported the system to achieve more efficient, complete, and stable pollutant removal performance. This study provides a theoretical basis and data support for optimizing the application and optimization of ABSS in aquaculture effluent treatment.