Urine, a typical wastewater, produced in urban areas and aerospace ships can be used to power microbial fuel cells (UMFCs) which are bio-electrochemical systems that may be used to recover precious energy from urine. The anode is a control factor that defines the performance of dual-chamber UMFCs to a large extent. Therefore, it has been a hot research topic for a long time to find the right materials and effective modification methods for improving the anodes’ performance. Graphene modification is one of the most promising anode modification methods and therefore in this paper the influences of electrodeposition time on the graphene-modified anode are experimentally investigated. It is found that there exists an optimum time for electrodeposition and this optimum time was found to be 60 s under our testing conditions. This anode, denoted as the 60-GN, has greater uniformly distributed graphene attachment and better electrochemical performance. The resistance of the 60-GN is 45 Ω. Equipped with this anode, the chemical oxygen demand (COD) removal of the UMFC is 86.91 ± 2.6%, and the maximum voltage of the UMFC is as high as 467.52 ± 16 mV and the power density 4485.33 ± 0.35 mW·m^-3 which are all the highest among others. 16S rDNA amplicon sequencing is employed to identify the microbial community. Analysis shows that although the relative quantity of microbes is different due to the different growing environment, the dominant bacteria is Enterobacter.