To remove membrane fouling, a bio-electrochemical system that can generate a micro-electric field and micro-current was constructed. After 11 days of operation, the trans-membrane pressure difference of membrane modules in the open- and closed-circuit groups increased by 35.8 kPa and 6.2 kPa, respectively. The concentrations of total polysaccharide and protein in the open-circuit group were 1.8 and 1.1 times higher than those in the closed-circuit group, respectively. In addition, X-ray photoelectron spectroscopy and thermogravimetric analysis showed that inorganic crystals such as calcium carbonate were present on the membrane surface, and the concentration of calcium ion in the control group was 14.7 times that of the experimental group. High-throughput sequencing demonstrated that the enrichment of some electroactive bacteria and other microorganisms has a positive effect on the control of membrane fouling. Therefore, this system can effectively alleviate membrane fouling of a bioreactor, by targeting the membrane foulants.