The present invention discloses a method for modifying a carbon nanotube electrode interface, which modifies carbon nanotubes used as a neuron-electrode interface by performing three stages of modifications and comprises the steps of: carboxylating carbon nanotubes to provide carboxyl functional groups and improve the hydrophilicity of the carbon nanotubes; acyl-chlorinating the carboxylated carbon nanotubes to replace the hydroxyl functional groups of the carboxyl functional groups with chlorine atoms; and aminating the acyl-chlorinated carbon nanotubes to replace the chlorine atoms with a derivative having amine functional groups at the terminal thereof. The modified carbon nanotubes used as the neuron-electrode interface has lower impedance and higher adherence to nerve cells. Thus is improved the quality of neural signal measurement. The present invention also discloses a microelectrode array, wherein the neuron-electrode interface uses carbon nanotubes modified according to the method of the present invention.