Nitrate removal from low carbon-to-nitrogen ratio (C/N) wastewater has always been a knotty problem due to the deficiency of organics. Here, a novel iron-based chemical reduction and autotrophic denitrification (ICAD) system was developed. ICAD system could maintain average nitrate removal efficiency of 97.2% for 131 days with feeding 20.3 mg NO3--N/L at hydraulic retention time (HRT) of 24 h. The optimal operational conditions was further explored, and results demonstrated that average nitrate removal efficiency of 85.5% and 98.4% could be achieved at HRT of 12 h and 24 h (influent 20.3 mg NO3--N/L), while average nitrate removal efficiency could reach 96.3% at optimal HRT of 12 h (influent 10.3 mg NO3--N/L). Hydrogenophaga, which can carry out hydrogenotrophic denitrification, showed a positive correlation with nitrate removal efficiency of the ICAD system. Low cost and simple operation make the ICAD system suitable for large-scale application.