An anoxic/oxic membrane bioreactor (MBR) and three side-stream reactor (SSR) coupled membrane bioreactors were operated in parallel to investigate effects of dissolved oxygen (DO) level in SSR on sludge reduction and microbial community structure of SSR-MBAs. The four MBAs were equally efficient in COD and ammonium nitrogen removal. The anaerobic and micro-aerobic SSR favored nitrogen removal through denitrification, simultaneous nitrification and denitrification and autochthonous substrate release as carbon source. The microaerobic SSR achieved greatly higher sludge reduction efficiency (61.1%) than anaerobic (37.3%) and aerobic SSR (7.9%). Micro-aerobic SSR obtained the highest endogenous decay constant (0.035 d(-1 )) compared to anaerobic (0.023 d(-1 )) and aerobic SSR (0.015 d(-1 ) ). High-throughput sequencing results revealed that anaerobic SSR enriched hydrolytic and fermentative bacteria, aerobic environment favored the growth of slow-growing bacteria, and micro-aerobic SSR stimulated biological activities of both anaerobic and aerobic bacteria.