Anode modification is a useful method to increase the performance of microbial fuel cells (MFCs). By using the electrochemical deposition method, Fe3O4 and polypyrrole (PPy) were polymerized on a carbon felt anode to prepare Fe3O4-PPy composite modified anodes. In order to ascertain the effect of electrodeposition time on characteristics of the modified electrode, the preparation time of the modified electrode was adjusted. The modified anodes were used in MFCs, and their performances were evaluated by analyzing the electricity generation performance and sewage treatment capacity of MFCs. Experimental results indicated that the Fe3O4-PPy composite modified anodes could enhance the power production capacity and sewage treatment efficiency of MFC effectively. In particular, when the deposition time was 50 min, the modified anode could significantly improve the MFC performance. In this case, the steady-state current density of MFC increased by 59.5% in comparison with that of the MFC with an unmodified carbon felt anode, and the chemical oxygen demand (COD) removal rate was 95.3% higher than that of the unmodified anode. Therefore, the Fe3O4-PPy composite is an effective material for electrode modification, and a good anode modification effect can be obtained by selecting the appropriate electrodeposition time.