Improving the performance of anode is a crucial step for increasing output power of marine sediment microbial fuel cells (MSMFCs) to drive marine monitor to work for a long term on the ocean floor. A pyrolyzed iron phthalocyanine modified multi-walled carbon nanotubes composite (FePc/MWCNTs) has been utilized as a novel nodified anode in the MSMFC. Its structure of the composite modified anode and electrochemical performance have been investigated respectively in the paper. There is a substantial improvement in electron-transfer efficiency from the bacteria biofilm to the modified anode via the pyrolyzed FePc/MWCNTs composite based on their cyclic voltammetry (CV) and Tafel curves. The electron transfer kinetic activity of the FePc/MWCNTs-modified anode is 1.86 times higher than of the unmodified anode. The maximum power density of the modified MSMFC was 572.3 ± 14 mW m −2, which is 2.6 times larger than the unmodified one (218.3 ± 11 mW m −2). The anodic structure and cell scale would be greatly minimized to obtain the same output power by the modified MSMFC, so that it will make the MSMFC to be easily deployed on the remote ocean floor. Therefore, it would have a great significance for us to design a novel and renewable long term power source. Finally, a novel molecular synergetic mechanism is proposed to elucidate its excellent electrochemical performance.