Four vertical-flow CWs (VFCWs) with different substrates and aeration conditions were studied on nutrient-removal capacity from synthetic wastewater. Zeolite substrate VFCWs (none-aerated: VFCW-1, aerated: VFCW-3) paralleled with ceramsite (none-aerated:VFCW-2, aerated: VFCW-4) were used to study the removal efficiencies of N and organics, the bacterial community, and the related functional genes. The results indicated that the pollutant removal efficiency was significantly enhanced by intermittent aeration. VFCW-4 (ceramsite with aeration) demonstrated a significant potential to remove NH4+-N (89%), NO3--N (78%), TN (71%), and COD (65%). VFCW-3 and VFCW-4 had high abundances of Amx, amoA, and nirK genes, which was related to NH4+-N and NO2--N removal. The microbial diversity and structure varied with aeration and substrate conditions. Proteobacteria, Actinobacteria, Candidatus, and Acidobacteria were the main bacteria phyla, with the average proportion of 38%, 21%, 19%, and 7% in the VFCWs. Intermittent aeration increased the abundance of Acidobacteria, which was conducive to the removal of organic matters. Overall, ceramsite substrate combined with intermittent aeration has a great potential in removing pollutants in VFCWs.