Enhancing the electrochemical performance of anode is a critical step for improving the power output of marine benthic microbial fuel cells (BMFCs). An active anode involving the akaganeite (β‐FeOOH)‐coated carbon felt was proposed in present study. Results showed that electrochemical performance of modified anode was significantly improved. The peak current density of oxidation reaction increased from 0.664 to 6.107 A m−2. The exchange current density was improved from 11.75 × 10−3 to 151.36 × 10−3 mA cm−2. Electron transfer resistance decreased from 13.4 to 1.407 Ω, while the surface capacitance dramatically increased. The maximum power density of the BMFCs equipped with modified anode approached to 504.2 mW m−2, 2.3 times higher than that with unmodified anode. Moreover, relative abundance of dissimilatory iron reducing bacteria (DIRB) on the modified anode increased. Finally, a molecule synergetic mechanism containing electrostatic interaction and bacteria recognition between DIRB and β‐FeOOH was proposed to interpret the improvement of modified anode.