The occurrence of biological pollution in MFC can cause serious problems such as hindered proton transfer, increased cathode Ohm and charge transfer resistance, and affect the stability and sustainability of MFC power generation. This study investigated the possible biological control of biological contamination on MFC anode biofilms and proton membranes by interfering with microbial energy metabolism. The results showed that the highest voltage of the low concentration (50ug/L) uncoupling agent increased by 21.8% and 24.7%, and the maximum power density increased by 72.2% and 58.8%, respectively. The inhibition of ATP synthesis by uncoupling agents leads to a decrease in the biomass of biofilms, reducing loose EPS in EPS and dissolved substances in anode solution. The proton membrane properties showed that the proton membrane conductivity and ion exchange capacity of the uncoupling agent group MFC increased by 11.6%, 20.3%, and 60.2%, 84.1%, respectively. At the same time, the thickness of the electrically active biofilm on the uncoupling agent electrode and the secretion of extracellular polymer (EPS) were significantly reduced, but the relative abundance of Geobacter was 169% and 86.8% higher than that of the blank group MFC, respectively. Overall, uncoupling agents can simultaneously reduce the operating cost of MFC and improve the performance of wastewater MFC.