The plants effect in subsurface flow constructed wetlands (SSF-CWs) is controversial, especially at low temperatures. Consequently, several SSF-CWs planted with Iris pseudacorus (CWI) or Typha orientalis Presl. (CWT) and several unplanted ones (CWC) were set up and fed with secondary effluent of sewage treatment plant during the winter in Eastern China. The 16S rDNA Illumina Miseq sequencing analysis indicated the positive effects of I. pseudacorus on the bacterial community richness and diversity in the substrate. Moreover, the community compositions of the bacteria involved with denitrification presented a significant difference in the three systems. Additionally, higher relative abundances of nitrifying bacteria (0.4140%, 0.2402% and 0.4318% for Nitrosomonas, Nitrosospira and Nitrospira, respectively) were recorded in CWI compared with CWT (0.2074%, 0.0648% and 0.0181%, respectively) and CWC (0.3013%, 0.1107% and 0.1185%, respectively). Meanwhile, the average removal rates of NH4+-N and TN in CWI showed a prominent advantage compared to CWC, but no distinct advantage was found in CWT. The hardy plant I. pseudacorus, which still had active root oxygen release in cold temperatures, positively affected the abundance of nitrifying bacteria in the substrate, and accordingly was supposed to contribute to a comparatively high nitrogen removal efficiency of the system during the winter.