Improving the performance of anode is a crucial step for increasing power output of marine sediment microbial fuel cells (SMFCs). A multi-walled carbon nanotube/polyaniline (MWCNTs/PANI) modified anode was prepared by the way of electrochemical deposition and its electrochemical performance is investigated in this paper. Result shows that the wettability of carbon felt becomes better and the number of bacteria (9.52 × 1012 m−2) on anode biofilm is increased respectively, which is 9 times higher than that of the unmodified. The anti-polarization ability of the modified anode increases significantly and its kinetic activity of electron transfer increases 4 times. Its exchange current density is 3.62 × 10−5 A cm−2. The maximum power density of the modified SMFC reaches 527.0 mW m−2, which is 4 times higher than that of the unmodified one. Finally, a novel molecular synergistic mechanisms for the enhanced SMFC is also presented, based on the higher bacteria number, the capacitive performance of PANI, the hydrogen bond interaction and higher conductivity of MWCNTs. This excellent electrochemical performance makes the MWCNTs/PANI composite be a potential choice for higher output SMFC.