The anaerobic/oxic/anoxic simultaneous nitrification, denitrification and phosphorus removal process (AOA-SNDPR) is a promising technology for enhanced biological wastewater treatment and in situ sludge reduction. Herein, effects of aeration time (90, 75, 60, 45, and 30 min, respectively) on the AOA-SNDPR were evaluated including simultaneous nutrients removal, sludge characteristics, and microbial community evolution, where the role of a denitrifying glycogen accumulating organisms, Candidatus_Competibacter, was re-explored given its overwhelming dominance. Results revealed that nitrogen removal was more vulnerable, and a moderate aeration period of 45–60 min favored nutrients removal most. Low observed sludge yields (Yobs) were obtained with decreased aeration (as low as 0.02–0.08 g MLSS/g COD), while MLVSS/MLSS got increased. The dominance of Candidatus_Competibacter was identified as the key to endogenous denitrifying and in situ sludge reduction. This study would aid the low carbon- and energy-efficient aeration strategy for AOA-SNDPR systems treating low-strength municipal wastewater.