In order to improve the degradation of organics in biogas slurry and electricity production of Microbial Fuel Cell (MFC), the combination of nano-Fe3O4 with MFC was proposed, loading nano-Fe3O4 on anode carbon felt (Fe3O4@carbon felt) and loading nano-Fe3O4 on biochar (Fe3O4@biochar) into the anode chamber. The performance of MFCs were comparatively studied. The results showed that the MFC both loading methods could successfully start, and the power production efficiency was much higher than that of the blank experiment without the intervention of nano-Fe3O4, with the maximum voltage of 699 and 707 mV, respectively, and the both maximum voltage value lasted up to 10 d. The maximum power density was increased by 43% and 31% in the Fe3O4@carbon felt (700 mW/m2) and Fe3O4@biochar (578 mW/m2) approaches, respectively, compared to that MFC without the use of Fe3O4 nanoparticles. The highest chemical oxygen demand (COD) degradation rate of 51.76% was obtained by using Fe3O4@carbon felt as the anode electrode; the direct application of Fe3O4@biochar had the greatest effect on the degradation of ammonium nitrogen, which decreased from (6800.14±57.86) mg/L to (689.14±37.29) mg/L after the application of Fe3O4@biochar, with a degradation rate of 89.87%.The microbial community structure of the MFC with the participation of nano-Fe3O4 tended to be rationalized, and both participation methods stimulated the growth of the main hydrolytic bacteria Clostridia. With the position of nano-Fe3O4 changing, the relative abundance of Clostridia in the MFC with Fe3O4@biochar directly inputting into the anode chamber and the MFC with Fe3O4@carbon felt as the anode electrode reached to 61.11% and 50.98%, respectively. Both had the highest content of Betaproteobacteria in electroactivation and denitrifying bacteria Sporosarcina was found on the post-reaction carbon felt.