An advanced electrodialysis fermentation system was set up to remove ammonium during hydrogen fermentation. When the voltage was increased from 0 to 6 V, the average ammonium removal rate was improved from 8.7 to 31.1 mg/L/h at an initial ammonium concentration of 3000 mg/L. A model based on the Nernst-Plank equation and porous media properties of ion exchange membranes was successfully implemented to predict the ammonium removal performance. When such a system was fed with synthetic wastewater at an ammonium concentration of 3000 mg/L for hydrogen fermentation, a significant increase in specific hydrogen yield was observed in the experiment group at 4 V. Specific hydrogen yield was 225.0 mL/g glucose, this value is 47.9% higher than the control. Moreover, ammonium concentration in experiment group was reduced to 701.6 mg/L at 72 h when voltage was set at 4 V, which is 63.7% lower than that in 0 V experiment group.