Abstract An amine-terminated ionic liquid (IL-NH 2 ) is applied to functionalize carbon nanotubes (CNTs) for improving the interfacial electron transfer of Shewanella putrefaciens (S. putrefaciens) anode in Microbial fuel cells (MFCs). The introduction of thin layer of ILs does not change the morphology of CNTs a lot but increases surface positive charges as well as nitrogen functional groups of the CNTs based anode. The CNT-IL composite not only improves the adhesion of S. putrefaciens cells but also promotes both of the flavin-mediated and the direct electron transfer between the S. putrefaciens cells and the anode. It is interesting that the CNT-IL is more favorable for the mediated electron transfer than for the direct electron transfer. The CNT-IL/carbon cloth anode delivers 3-fold higher power density than that of CNT anode and shows great long-term stability in the batch-mode S. putrefaciens MFCs. This CNT-IL could be a promising anode material for high performance MFCs.