Microcystins (MCs) pollution caused by cyanobacteria harmful blooms (CHBs) has posed short- and long-term risks to aquatic ecosystems and public health. Constructed wetlands (CWs) have been verified as an effective technology for eutrophication but the removal performance for MCs did not achieve an acceptable level. CWs integrated with microbial fuel cell (MFC-CWs) were developed to intensify the nutrient and Microcystin-LR (MC-LR) removal efficiencies in this study. The results indicated that closed-circuit MFC-CWs (T1) exhibited a better NO₃⁻-N, NH₄⁺-N, TP and MC-LR removal efficiency compared to that of open-circuit MFC-CWs (CK, i.e., traditional CWs). Therein, a MC-LR removal efficiency of greater than 95% was observed in both trials in T1. The addition of sponge iron to the anode layer of MFC-CWs (T2) improved only the NO₃⁻-N removal and efficiency bioelectricity generation performance compared to T1, and the average effluent MC-LR concentration of T2 (1.14 μg/L) was still higher than the provisional limit concentration (1.0 μg/L). The microbial community diversity of T1 and T2 was simplified compared to CK. The relative abundance of Sphingomonadaceae possessing the degradation capability for MCs increased in T1, which contributed to the higher MC-LR removal efficiency compared to CK and T2. While the relative abundance of electrochemically active bacteria (EAB) (i.e., Desulfuromonadaceae and Desulfomicrobiaceae) in the anode of T2 was promoted by the addition of sponge iron. Overall, this study suggests that integrating MFC into CWs provides a feasible intensification strategy for eutrophication and MCs pollution control.