As the electrode structure has a great effect on the performance of the benthic microbial fuel cell (BMFC), several graphite electrodes with different shapes (column, plane disk and tubular shape for example) are designed in this paper. The maximum power density (Pm) of BMFC-c and BMFC-d are 20.2 mW•m-2 and 14.9 mW•m-2 respectively, and the internal resistances are 333 Ω and 598 Ω respectively. Three cells are composed of three different sizes of graphite tubes, and their internal diameter of these electrodes are 2.5 cm (called it as BMFC-I for short); 1.0 cm (BMFC-II) and 0 cm (column shape for comparison, BMFC-III) respectively. Test results show that the Pm of BMFC-I, BMFC-II and BMFC-III are 13, 11 and 16 mW•m-2 respectively, and their internal resistances are 435 Ω, 488 Ω and 419 Ω respectively. Results show that the column structure electrode has a lower internal resistance and a higher power density than the disk and tubular structure electrode.