The characteristic of anode plays an important role in the performance of the microbial fuel cell (MFC). Thus, carbon nanotube (CN), flexible graphite (FG) and activated carbon (AC) were used as anode material in this study, and the performances of three MFCs (CN-MFC, FG-MFC and AC-MFC) were studied. The results show that CN is a kind of suitable material to be used as anode in the MFC. The maximal power densities of CN-MFC, FG-MFC and AC-MFC are 402,354 and 274 mW/m2, respectively. The CN-MFC shows a higher power density and coulombic efficiency compared with FG-MFC and AC-MFC. The CN-anode can reduce the internal resistance obviously. The internal resistances of CN-MFC, AC-MFC and FG-MFC are 263, 301 and 381 omega, respectively. The protein contents on the CN-anode, AC-anode and FG-anode are 149, 132 and 92 microg/cm2 after stable operation, and there is a positive relation between the protein content and internal resistance. The conductivity of the three types of MFCs from high to low was FG-MFC, CN-MFC and AC-MFC, which was accordant with the ohmic resistance. The stable times of CN-MFC, FG-MFC and AC-MFC, which were needed to measure the internal resistances, were 1800, 1200 and 300 s respectively.