Membrane fouling is an inevitable occurrence in the dual chamber microbial fuel cell (MFC). However, this study aims to investigate the potential role of uncoupling agents on MFC performance and proton membrane fouling. In the anode biofilm of MFC, the uncoupling agent could potentially prevent the energy generated from electron transfer in the respiratory chain from being utilized for ADP phosphorylation, leading to dissipation in the form of heat. This ultimately leads to a thinner biofilm and exacerbation of extracellular electron transfer (EET). Conversely, the control group exhibited continuous growth of anode microorganisms, leading to the formation of a relatively thicker biofilm on the electrode surface, resulting in larger numbers of dead cells and an increase in loose extracellular polymeric substances (EPS) content. This ultimately increases biological pollution of the proton membrane, which adversely impacts the electrochemical performance and application of the MFC process. This study provides valuable insights into the development of biofilm formation on proton membranes, highlighting the spatial and temporal differences of anodic biofilms. These insights can guide the design of more effective methods to apply uncoupling agents to alleviate proton membrane biofilm in the MFC process.