A 3-dimensional biofilm electrode reactor (3DBER) coupled with sulfur autotrophic denitrification system was developed by integrating with micro-electrocoagulation process. The novel process, namely MEC-3DBER-S, was set up to enhance the removal efficiency of nitrogen and phosphorus for the effluent of low C/N ratio from municipal wastewater treatment plant (WWTP). The characters of MEC-3DBER-S were compared with that of 3DBER under different current conditions. Moreover, the biofilm denitrifying bacteria community was also analyzed in MEC-3DBER-S system based on the library of nirS gene cloning technology. The results indicated that the removal efficiency of nitrogen and phosphorus are intensified in MEC-3DBER-S process as compared to 3DBER, especially the denitrification under the lower current conditions. Phosphorus removal efficiency could be improved by the sponge iron corrosion process that was induced by the function of current. The nitrogen and phosphorus removal efficiencies were reached about 75% and 78% respectively, which were 10% and 28% higher than that of 3DBER under the condition of C/N=1.5, HRT=8h, I=300mA. In addition, it was found that heterotrophic denitrifying bacteria, hydrogen autotrophic denitrifying bacteria, sulfur autotrophic denitrifying bacteria and iron autotrophic denitrification denitrifying bacteria simultaneously existed in MEC-3DBER-S system, which could respectively utilize organic carbon, H2, sulfur and Fe²⁺ as electron donors for denitrification. The denitrification efficiency could be improved and stabilized by the mutual complementation of the different electron donors. In the meantime, there would be the physical, chemical and biological effects that were resulted in more efficient for phosphorus removal in the system. Thus, a higher nitrogen and phosphorus removal efficiency could be guaranteed in MEC-3DBER-S process.