Abstract: To investigate the effects of intermittent aeration on nitrogen removal performance and microbial communities in constructed wetlands treating marine aquaculture effluent, two pilot-scale composite vertical-flow constructed wetland systems operated under intermittent aeration and natural conditions were established. Three aeration/non-aeration ratios (1 h∶23 h, 1 h∶11 h, and 1 h∶5 h) were tested in the intermittent aeration group. Physicochemical parameters were measured in the influent, effluent, and different substrate layers of the downflow and upflow units. In addition, bacterial 16S rRNA gene high-throughput sequencing was conducted on substrate samples collected during the stage with the optimal overall nitrogen removal performance. These measurements, combined with alpha/beta diversity analysis, environmental correlation analysis, and FAPROTAX functional prediction, allowed a comparison of the nitrogen removal characteristics and microbial responses of the marine constructed wetlands under the two operation modes. The results showed that: (1) the intermittently aerated constructed wetland exhibited significantly better removal of ammonia nitrogen, nitrite nitrogen, and total nitrogen than the naturally operated constructed wetland. The optimal overall nitrogen removal performance was achieved at an aeration/non-aeration ratio of 1 h∶5 h, with the highest removal efficiencies of 89%, 98%, and 70%, and final effluent concentrations of 0.14-0.17, 0.01-0.03, and 1.15-1.47 mg/L, respectively. In contrast, the naturally operated constructed wetland showed better nitrate nitrogen removal. (2) Intermittent aeration significantly increased the richness, evenness, and diversity of the microbial community, and resulted in a clear separation of microbial community structures between the two operation modes. (3) Dissolved oxygen was identified as a key environmental factor driving community differences, explaining 17.23% of the variation. Both redundancy analysis (RDA) and the Mantel test confirmed a significant correlation between dissolved oxygen and microbial community structure. (4) Functional prediction indicated that nitrification-related functions were relatively enriched in the intermittently aerated constructed wetland, whereas denitrification-related functions were stronger in the naturally operated constructed wetland. These findings demonstrate that intermittent aeration can synergistically enhance nitrogen removal performance and reshape microbial community structure and function in marine constructed wetlands by regulating dissolved oxygen gradients, thereby providing a theoretical basis for optimizing ecological treatment processes for marine aquaculture effluent.