Anode modification is an effective strategy for enhancing the electrochemical performance of microbial fuel cell (MFC). However, the impacts of the modified materials on anode biofilm development during MFC operation have been less studied. We prepared a novel PDA-Fe3O4-CF composite anode by coating original carbon felt anode (CF) with polydopamine (PDA) and Fe3O4 nanoparticles. The composite anode material was characterized by excellent hydrophilicity and electrical conductivity, and the anodic biofilm exhibited fast start-up, higher biomass, and more uniform biofilm layer after MFC operation. The MFC reactor assembled with the composite anode achieved a maximum power density of 608 mW m−2 and an output voltage of 586 mV, which were 316.4% and 72.4% higher than the MFC with the original CF anode, respectively. Microbial community analysis indicated that the modified anode biofilm had a higher relative abundance of exoelectrogen species in comparison to the unmodified anode. The PICRUSt data revealed that the anodic materials may affect the bioelectrochemical performance of the biofilm by influencing the expression levels of key enzyme genes involved in biofilm extracellular polymer (EPS) secretion and extracellular electron transfer (EET). The growth of the anodic biofilm would exert positive or negative influences on the efficiency of electricity production and electron transfer of the MFCs at different operating stages. This work expands the knowledge of the role that anodic materials play in the development and electrochemical performance of anodic biofilm in MFCs.