Abstract: Intermittent aeration in constructed wetlands is an efficient, environmentally friendly, and widely applied wastewater treatment technology. In this study, a series of experimental constructed wetland systems comprising IACWs operated with different aeration/rest time ratios (1:23, 1:11, and 1:5) and natural flow constructed wetlands (NFCWs) were employed to treat marine aquaculture effluent. Through physicochemical analyses and 16S rRNA gene sequencing, we compared nitrogen removal performance and microbial community characteristics between the two types of systems, aiming to elucidate the effects of intermittent aeration on treatment efficiency and microbial structure. The results demonstrated that IACWs achieved significantly higher removal efficiencies for ammonia nitrogen (NH₄⁺–N), nitrite nitrogen (NO₂⁻–N), and total nitrogen (TN) compared to NFCWs. Among the aeration strategies, the system with a 1:5 aeration/rest ratio exhibited the best performance, with removal rates of 89% for NH₄⁺–N, 99% for NO₂⁻–N, and 70% for TN. In contrast, nitrate nitrogen (NO₃⁻–N) removal was significantly higher in the naturally operated wetlands. Microbial diversity analysis revealed that IACWs supported significantly higher microbial richness and evenness than NFCWs. Although the species composition between the two systems was generally similar, their spatial distributions exhibited notable divergence. Dissolved oxygen (DO) emerged as a key environmental factor, with its differing levels across systems exerting a profound influence on microbial community structure and functional potential. Overall, IACWs showed superior potential for comprehensive nitrogen pollutant removal, providing a robust theoretical and technical foundation for optimizing operational strategies of constructed wetlands in marine aquaculture wastewater treatment.