Bioretention cell (BRC) and an enhanced system combining bioretention cell with microbial fuel cell (BRC-MFC) were used to treat domestic wastewater. Nitrogen removal characteristics and permeation characteristics of two systems were investigated by adjusting influent carbon/nitrogen ratio (C/N = 2–20). Results showed that nitrification and denitrification performances were mainly influenced by organic matter and system combination, which further effected the nitrogen removal. When optimal operating parameters were: electrode space of 30 cm, hydraulic load of 1.0 m3/(m2·d) and inlet/reaction time of 1/8 in BRC-MFC system, chemical oxygen demand (COD), total nitrogen (TN) and NH4+ removal efficiencies still reached 97.63, 64, and 42.26%, respectively and achieved high removal efficiency of organic matter and nitrogen simultaneously compared to the BRC system. Efficient supply of electron and phylogenetic diversity of bacterial communities in BRC-MFC process was the main reason to achieve deep denitrification removal. After the V3-V4 variable region of 16S rRNA gene was sequenced by the Miseq high-throughput sequencing method, introduction of MFC enhancement technology affected the microbial community structure in the system. The presence of MFC contributed to an increase in community diversity (from 14 to 19 phyla). The results provide a simple method without kinetic energy for simultaneous denitrification and steady infiltration of bioretention.