A new operating approach by reducing the aeration time while keeping high intensity was evaluated for enhanced nutrients removal and maintenance of granular stability. Three aerobic granular sequencing batch reactors (SBR) performing simultaneous nitrification, denitrification and phosphorus removal (SNDPR) were run at different aeration time (120, 90, and 60 min). Aerobic granules could remain their integrity and stability over long-term operation under high aeration intensity and different time, and shorter aeration time favored the retention of biomass, better settleability, and more production of extracellular polymeric substances (EPS). Besides, efficient and stable reactor performance for carbon and phosphorus were achieved, especially, enhanced nitrogen removal was obtained due to reduction of aeration time. Further exploration revealed that the aeration time shaped the bacterial community in terms of diversity, composition, as well as the distribution of functional groups involving carbon, nitrogen and phosphorus removal.