An integrated constructed wetland-microbial electrolysis cell (ICW-MEC) system was investigated for nitrogen removal under different pollution loads, hydraulic loads (HLRs), and aeration conditions. The treatment performance of each unit and the microbial community characteristics for nitrogen removal were elucidated. The results showed that, on average, 80% of NH4+-N, around 70% of nitrate nitrogen (NO3−-N), and 70% of total nitrogen (TN) were removed by the system under three pollution loads, with less influence by pollution loads. The high removal efficiencies of NH4+-N (81.8%), NO3−-N (71.4%), and TN (72.8%) indicated tolerable to high HLRs. The intermittent aeration negatively affected NH4+-N removal, while increasing NO3−-N and TN removals by 3.2–13.0% and 3.7–16.7%. The contribution efficiencies of the secondary unit to the removal of NH4+-N, NO3−-N, TN, and total organic carbon (TOC) reached 47.4%, 55.0%, 45.9%, and 38.8%, respectively. The distinct microbial communities existed in various units of the ICW-MEC system, which were strongly affected by environmental factors and shaped by diverse fillers and structures of the system. The dominant bacteria contributed to the efficient nitrogen removal performance of the ICW-MEC system. The three units exerted their advantages to ensure efficient and stable system operation.