Ni electrode was modified with graphene by the electrodeposition (ED) method to prepare an anode (anode-ED) for microbial fuel cell (MFC). Electrochemical and morphological characterizations of anode-ED along with the effects of anode modification on the MFC performance were investigated. The graphene modification based on cyclic voltammetric electrodeposition resulted in the decrease of charge transfer resistance (R-ct) and improved extracellular electron transfer efficiency of anode. The maximum power density obtained from the MFC equipped with anode-ED was 25.83 and 17.86 times larger than those of MFCs equipped with bare Ni anode and anode modified with graphene by traditional hydrothermal treatment method (anode-HT), respectively. The electrochemical impedance spectroscopy (EIS) analysis results indicated that the R-ct of anode decreased significantly after inoculation during the MFC operation. The improvement in power density was attributed to the decreasing R-ct and the biocompatibility of graphene modified on anode-ED surface. This study presented an effective electrodeposition method to make graphene-modified anodes, which could improve the MFC performance.