A traditional sequencing batch reactor (SBR) and two intermittently aerated sequencing batch reactors (IASBRs) were parallelly operated for treating digested piggery wastewater. Their microbial communities were analyzed, and the nitrogen removal performance was compared during the long–term run. IASBRs demonstrated higher removal rates of total nitrogen (TN) and ammonium nitrogen (NH -N) than the SBR, and also demonstrated higher resistance against TN shock load. It was found that the more switch times between aerobic/anoxic in an IASBR, the higher the removal rates of TN and NH –N. All the reactors were predominated by , and , which were considered to be species of denitrifiers, ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), respectively. However, the abundance and diversity was of great difference. Compared with SBR, IASBRs achieved higher abundance of denitrification–related bacteria. IASBR 1 with four aerobic/anoxic switch times was detected with 25.63% of , higher than that in IASBR 2 with two aerobic/anoxic switch times (11.57% of ), and much higher than that in the SBR (only 6.19% of ). IASBR 2 had the highest percentage of AOB, while IASBR 1 had the lowest percentage. The denitrifiers abundance was significantly positive correlated with the TN removal rate. However, the NH –N removal rate showed no significant correlation with the AOB abundance, but might relate to the AOB activity which was influenced by the average free ammonium (FA) concentration. was the only NOB genus detectable in all reactors, and were less than 0.03%.