The effects of aeration conditions on the nitrogen removal performance in conventional anaerobic-anoxic-oxic (A2/O) and side-stream activated sludge hydrolysis (SSH) reactors were investigated by changing the aeration intensity and dissolved oxygen (DO) concentration, and the changes in microbial community structures were also studied. The results showed that the nitrogen removal performance of the two reactors in low and medium DO concentrations was better than that in high DO concentration. Under the same influent condition, the nitrogen removal performance of SSH reactor was better than that of A2/O reactor, and its effluent concentration met the Class A standard. High-throughput sequencing results showed that low to medium DO concentrations were more beneficial for the growth of the microorganisms for nitrogen removal. A higher relative abundance of denitrifying microorganisms was observed in SSH reactor compared to A2/O reactor. Therefore, Maintaining low to medium DO concentrations of aeration conditions is conducive to the SSH process to achieve effective nitrogen removal performance and the growth of microorganisms for nitrogen removal.