Nitrate pollution in water is a worldwide health and environmental concern. Biological nitrate removal of wastewater is widely used countering eutrophication of water bodies; however it could be troublesome and expensive when influent carbon source is insufficient. Here we present a novel process, the microbial fuel cell (MFC)-resistance-type electrical stimulation denitrification process (RtESD) using microbial weak electricity originated from the wastewater, to enhance nitrate removal. Results show that the optimal nitrate dependent denitrification rate (0.027 mg N/L·h) and nitrate removal efficiency (98.1%) can be achieved; partial autotrophic denitrification was enhanced in RtESD under stimulation of 0.2 V of microbial weak electricity (MWE). Aromatic proteins also increased in the presence of 0.2 V MWE stimulation according to three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy profiles, indicating that electron transfer could be improved in the case of MWE stimulation. Furthermore, the microbial community structure and diversity analysis results demonstrated that MWE stimulation inhibited the heterotrophic denitrifying bacteria and activated the autotrophic denitrifying bacteria in RtESD. Two hypotheses, enhancement of electron transfer and improvement of microorganism activity, were proposed regarding to the MWE stimulated pathways. This study provided a promising method utilizing MWE derived from wastewater to improve the denitrification rate and removal efficiency of nitrate-containing wastewater treatment processes.