In this study, a laboratory-scale system combined a vertical flow constructed wetland (VF) with a horizontal flow constructed wetland (HF), which was used to treat the secondary effluent of a wastewater treatment plant. Removal efficiencies of 67.02%, 89.80%, 90.31% and 75.38% were achieved by the system for chemical oxygen demand (COD), ammonium nitrogen (NH4+-N), total nitrogen (TN) and total phosphorus (TP), respectively. The VF showed much higher average loading rates of COD, TP, NH4+-N and TN (7.96 g/m2/d, 0.076 g/m2/d, 0.31 g/m2/d and 0.99 g/m2/d) than in HF (0.65 g/m2/d, 0.016 g/m2/d, 0.25 g/m2/d and 0.50 g/m2/d), during the stable operation period. Biodegradation played a major role in pollutant removal, especially for COD and TN. The results of bacterial community analysis indicated that heterotrophic denitrifying bacteria (Hydrogenophaga and Flavobacterium) were the dominant contributors for nitrogen removal in the VF, while heterotrophic denitrifying bacteria (Rhodobacter, Flavobacterium and Dechloromonas) and the autotrophic denitrifying bacteria Sulfurimonas played the principal roles for nitrogen removal in the HF. Redundancy analyses showed that COD and NH4+-N were the important factors affecting the distribution of nitrogen removal bacteria in the VF, while pH, dissolved oxygen and oxidation-reduction potential were the key factors influencing the distribution of nitrogen removal bacteria in the HF.