To screen high-efficiency purification systems for aquaculture effluent from Litopenaeus vannamei high-position ponds, we utilized four biological filter media were utilized including sponge (HM), modified high-density polyethylene (K5), ceramic stone (TC), and fiber ball (XW) to immobilize Spirulina platensis and Chlorella vulgaris, respectively. The purification performance of different combinations on aquaculture effluent was systematically compared. Results showed that fiber balls yielded the highest cell immobilization density for both microalgae, reaching 1.78×10⁸ cells·g⁻¹ for S. platensis and 4.79×10⁸ cells·g⁻¹ for C. vulgaris, respectively. Moreover, C. vulgaris exhibited a significantly higher attachment density than S. platensis across all tested media (p<0.05). For a given microalga, the filter medium type significantly influenced the removal rates of all water quality parameters, with XW demonstrating the best performance. Under the same filter medium, C. vulgaris showed significantly higher removal rates of total nitrogen (TN), total phosphorus (TP) and chemical oxygen demand (COD) than S. platensis, whereas S. platensis exhibited a significantly higher removal rate of total suspended solids (TSS) (p<0.05). Two-way ANOVA revealed significant interactive effects between microalgal species and filter medium type on the removal rates of total inorganic nitrogen (TIN), orthophosphate ( ${\mathrm{P}\mathrm{O}}_4^{3-}\text{-}\mathrm{P}$), TN, TP, TSS, and COD (p<0.01). The fiber ball-C. vulgaris system achieved the highest removal rates for TIN (95.29%), ${\mathrm{P}\mathrm{O}}_4^{3-}\text{-}\mathrm{P}$ (96.25%), TN (55.78%), and COD (75.09%); the fiber ball-S. platensis system achieved the highest removal rate for TSS (85.65%). Therefore, targeted purification of aquaculture effluent can be realized by precisely selecting microalga-filter material combinations according to the target pollutants. This coupled system not only offers a key technological solution for resource utilization and discharge standard compliance of high-pond aquaculture effluent, but also corresponds to the current strategic needs for green, low-carbon, and circular development in aquaculture. It shows great potential for engineering applications in various scenarios such as ecological purification ponds.