Nitrogen pollution of surface water is still a critical issue worldwide. In this study, a total of four treatments were conducted in horizontal subsurface flow constructed wetlands (HSSFCWs) to explore the removal rate of nitrogen in the carbon-deficient wastewater, including combination of aeration and external carbon source (CW_CA), external carbon source (CW_C), aeration (CW_A), and control group without aeration and carbon source (CW_CK). Results showed that the removal rates of total nitrogen (TN) in the enhanced treatments were increased compared with CW_CK. The highest removal rates of COD (66.56%), NH4+-N (73.51%), NO3−-N (79.31%), and TN (76.19%) were observed in the CW_CA treatment. The bacterial community structure at the fore and rear ends of HSSFCWs was simultaneously changed in the CW_CA and CW_C treatments, respectively. The highest richness index at both the fore and rear ends of HSSFCWs was found in the CW_CA treatment. The richness and diversity indices of CW_C declined at the fore ends of HSSFCWs, but increased at the rear ends of HSSFCWs. Furthermore, the functional bacteria and genes significantly changed among different treatments. At the fore ends of HSSFCWs, the highest relative abundance of nitrifiers and absolute abundance of amoA and nxrA were obtained in CW_A, and the highest relative abundance of denitrifying bacteria and absolute abundance of nirS, nirK, nosZ were found in CW_C. However, at the rear ends of HSSFCWs, the highest relative abundance of nitrifiers and denitrifying bacteria as well as the absolute abundance of related genes were also observed in the CW_CA treatment. Overall, CW_CA improved the nitrogen removal rate by increasing the abundance of nitrogen-converting functional microbes and the genes associated with nitrification and denitrification.