Objective Implantable brain computer interface has been widely used in the treatment of neurological diseases, where the effectiveness of the treatment depends on the electrodes in contact with the neural tissue. Compared with the electrodes made of rigid materials, the carbon based microfiber electrodes have small scale, good biocompatibility and small tissue inflammatory reaction. It can reduce the foreign body reaction after implantation, improve the signal-to-noise ratio of nerve recording signals, and maintain stable electrode characteristics for a long time.Methods A modification method of flexible carbon nanotubes (CNTs) fiber electrode was designed in this paper. Poly(3,4-ethylenedioxythiophene) (PEDOT) films can be deposited on CNTs fiber electrode as microelectrode coating by electrochemical polymerization. In order to prove that the modified coating has good mechanical stability on the electrode surface, we treated the modified electrode with ultrasonic treatment. In addition, PEDOT films were deposited on ITO glass to evaluate the biocompatibility of PEDOT films.Results PEDOT coating deposited on the surface of CNTs fiber electrode in constant current mode reduced the electrochemical impedance of the electrode and improved the electrochemical performance of the electrode. The longer PEDOT deposition time, the more obvious the reduction of impedance. After ultrasonic treatment, the electrochemical impedance of the electrode did not change significantly, indicating that there was less peeling of PEDOT coating after ultrasonic treatment, which proved that the modified coating had good mechanical stability on the electrode surface. Finally, cell experiments show that PEDOT film has the same cell compatibility as ITO conductive glass.Conclusion PEDOT film can improve the stability of CNTs fiber electrode, and is expected to improve the service life and reliability of brain computer interface system. It has the prospect of application in long-term recording of neuroelectrical signals.