Polyaniline (PANI) was electropolymerized on the surface of macroporous graphite felt (GF) followed by the electrophoretic deposition of carbon nanotubes (CNTs). The as-prepared macroporous material was characterized by scanning electron microscopy, water contact angle goniometry and electrochemical techniques. Upon the modification of PANI, a rough and nano-cilia containing film is coated on the surface of the graphite fibers, transforming the surface from hydrophobic to hydrophilic. The subsequent modification by CNTs increases the effective surface area and electrical conductivity of the resulting material. The power output of a mediator-free dual-chamber microbial fuel cell (MFC) constructed from the GF anode and an exoelectrogen Shewanella putrefaciens increases drastically with the CNT modification. The CNT/PANI/GF MFC attains an output voltage of 342 mV across an external resistor of 1.96 kΩ constant load, and a maximum power density of 257 mW m−2, increased by 343% and 186%, compared to that of the pristine GF MFC and the PANI/GF MFC, respectively. More bacteria are attached on the CNT/PANI/GF anode than on the PANI/GF anode during the working of the MFC. This strategy provides an easy scale-up, simple and controllable method for the preparation of high-performance and low-cost MFC anodes.