The treatment of micro-polluted water via a constructed wetland (CW), such as fishpond aquaculture wastewater, encounters problems such as low effectiveness and poor stability. In this study, an emerging algae-bacteria microbial fuel cell (AB-MFC) was coupled with CW to strengthen the treatment of fishpond aquaculture wastewater. Compared with those in the control group (without AB-MFC), the average removal efficiencies of chemical oxygen demand, total phosphorus, total nitrogen, NH4+-N, NO3—N, and NO2—N in AB-MFC-CW were enhanced by 23.84%, 21.44%, 15.07%, 16.91%, 15.02%, and 9.83%, respectively. High-throughput sequencing revealed that Acinetobacter, Cyanobium, Pseudomonas, and Ottowia were relatively abundant on the electroactive AB biofilm. Geobacter, Aminicenantales and Clostridium grew well in the MFC Anode. The economic evaluation indicated that energy consumption per ton of sewage treatment was 0.0045 kWh/m3. These results confirm that the AB-MFC-CW is feasible for enhancing the treatment of aquaculture wastewater at both technical and economic levels through pilot-scale verification.