Cobalt-modified molybdenum dioxide nanoparticles highly dispersed on nitrogen-doped carbon nanorods (Co-MoO/NCND), are synthesized from anilinium trimolybdate dihydrate nanorods, for the performance improvement of microbial fuel cell based on a mixed bacterial culture. Electrochemical measurements demonstrate that the as-synthesized Co-MoO/NCND exhibits excellent electrocatalytic activity for the charge transfer on anode, providing the cell with a maximum power density of 2.06 ± 0.05 W m, which is strikingly higher than the bare carbon felt anode (0.49 ± 0.04 W m). The excellent performance of Co-MoO/NCND is ascribed to the increased electronic conductivity of carbon nanorods by N-doping, the high ability of MoO to enrich electroactive bacteria, as demonstrated by high-throughput sequencing, and the enhanced activity of MoO by Co-modifying toward redox reactions in electroactive bacteria. This report provides a new concept of anode electrocatalyst fabrications for the application of microbial fuel cells in electricity generation and wastewater treatment.