Microbial fuel cell (MFC) on the ocean floor is a kind of novel energy- harvesting device that can be developed to drive small instruments to work continuously. The shape of electrode has a great effect on the performance of the MFC. In this paper, several shapes of electrode and cell structure were designed, and their performance in MFC were compared in pairs: Mesh (cell-1) vs. flat plate (cell-2), branch (cell-3) vs. cylinder (cell-4), and forest (cell-5) vs. disk (cell-6) FC. Our results showed that the maximum power densities were 16.50, 14.20, 19.30, 15.00, 14.64, and 9.95 mWm−2 for cell-1, 2, 3, 4, 5 and 6 respectively. And the corresponding diffusion-limited currents were 7.16, 2.80, 18.86, 10.50, 18.00, and 6.900 mA. The mesh and branch anodes showed higher power densities and much higher diffusion-limited currents than the flat plate and the cylinder anodes respectively due to the low diffusion hindrance with the former anodes. The forest cathode improved by 47% of the power density and by 161% of diffusion-limited current than the disk cathode due to the former’s extended solid/liquid/gas three-phase boundary. These results indicated that the shape of electrode is a major parameter that determining the diffusion-limited current of an MFC, and the differences in the electrode shape lead to the differences in cell performance. These results would be useful for MFC structure design in practical applications.