Characteristics of nitrogen removal and nitrous oxide (N2O) emission in the multiple anoxic/aerobic (AO) process were examined in three sequencing batch reactors (SBRs) with different anoxic durations (50 min, SBRH; 40 min, SBRM; 30 min, SBRL) and a fixed aerobic duration of 30 min. The highest total inorganic nitrogen removal percentage of 85.8% was obtained in SBRH, while a minimum N2O emission factor of 1.9% was obtained in SBRL. During nitrification batch experiments, the N2O emission factor and emission rate were both lower in SBRH than SBRL. More N2O production was obtained during denitrification in SBRH when denitrifiers utilized intracellular organic carbon. Nitrite reduction by heterotrophs was the main N2O production pathway during simultaneous nitrification and denitrification in SBRH and SBRL, with the N2O emission factor of 31.3% and 36.3%, respectively. Adequate anoxic duration and lowering aerobic nitrite concentrations could be adopted to mitigate N2O emission in the multiple AO process. The dominant microorganisms at the phylum level in all reactors were Proteobacteria and Bacteroidetes, while the abundance of Nitrospira was the highest in SBRH with relatively lowest dissolved oxygen concentrations.