The ecological safety problems caused by nitrogen pollution in water have attracted much attention. An organic carbon source is the key factor that restricts nitrogen removal in low COD/total nitrogen (C/N) sewage. In this study, iron‑carbon micro-electrolysis carrier was used for micro-electrolysis combined with biological denitrification (MEBD) of samples under low C/N conditions (C/N = 1.33). The nitrogen removal performance, the factors influencing nitrogen removal, and the underlying mechanisms of the removal system are studied using the response surface curve method and high-throughput sequencing. The results showed that when pH was 7, the dosage of denitrifying bacteria was 5%, and the dosage of iron‑carbon was 10%, the optimal denitrification effect for low C/N wastewater was 97.86% and 97.72% for total nitrogen and COD removal in 20 days, respectively. The addition of an iron‑carbon filler changed the community abundance and species diversity in MEBD system, and the structure of the dominant denitrifying bacteria changed. Moreover, hydrogen autotrophic denitrifying bacteria had been identified in the system. The synergistic effect of MEBD coupled denitrification system was due to the combined action of autotrophic denitrification, heterotrophic denitrification, micro–electrolysis, and electrochemical reduction. These findings provide a theoretical basis and technical support for nitrogen remediation of low C/N sewage.