Inhibitory effect of electron mediator AQDS on Geobacter metallireducens nanowire in microbial fuel cell (MFC) was studied. In the culture process of G. metallireducens with Fe(OH)3 as electron acceptor, the concentration of reduction product Fe (II) in solution without AQDS is higher than that with AQDS after 10 days, due to the formation of microbial nanowires. The effects of nanowire on electron transfer efficiency and power generation characteristic were studied using double chamber MFC reactor. The transfer efficiency between biofilm and electrodes was increased by nanowire, which increases maximum output voltage of MFC from 321 mV to 442 mV. The nanowire biofilm electrode has the bigger cyclic voltammetry curve peak, smaller activation resistance and stronger current response signal through electrochemical measurement, which indicated that the nanowire enhanced the electrochemical activity of the electrode.