In this study, an intermittent-aerated subsurface flow constructed wetland (SFCW) A was set up to assess its performance in decentralized rural sewage treatment. A conventional SFCW B and a subsurface wastewater infiltration system (SWIS C) were also constructed for comparison. Alternate anaerobic and aerobic conditions were well developed by intermittent aeration. High removal of organic pollutants (29.3gm(-2)d(-1)), ammonium nitrogen (3.5gm(-2)d(-1)) and total nitrogen (3.3gm(-2)d(-1)) were obtained simultaneously in SFCW A compared with SFCW B and SWIS C. Fluorescence in situ hybridization analysis proved that the intermittent aeration obviously enhanced the growth of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in SFCW A. These results suggest that intermittent aeration strategy is reliable to enhance the performance of SFCWs in decentralized rural sewage treatment.