A three-chamber electrodialysis bioreactor comprising fermentation, cathode and anode chambers was proposed to remove in situ volatile fatty acids during hydrogen fermentation. The electrodialysis voltage of 4 V resulted in a volumetric hydrogen productivity of 1878.0 mL/L from the fermentation chamber, which is 55.4% higher than that (1208.5 mL/L) of the control group without voltage applied. Gas production was not observed in the cathode and anode chambers throughout fermentation. By applying different voltages (0-6 V), the hydrogen content accumulated to 54.6%-84.7%, and it exhibited increases of 7.1%-66.4% compared with that of the control. Meanwhile, the maximum concentrations of acetate and butyrate in the fermentation chamber decreased to 10.3 and 13.1 mmol/L at a voltage of 4 V, respectively, which are 68.0% and 62.4% lower than that for the control.