This research is to investigate the character of membrane separation and removal nutrients by the changes of operation cycles through submerged membrane coupled sequencing batch reactor (SM-SBR) to minimize the membrane fouling and remove organic and nutrients simultaneously. When SM-SBR process operation cycle 6-12 hr/cycle, the membrane fouling was decreased while the operation period was extended. Image analysis of the mixed liquor in SM-SBR with anoxic phase showed greatly higher number of suspended particles than that of the membrane bioreactor (MBR) without anoxic phase. Bound extracellular polymeric substances (EPS) in the mixed liquor of SM-SBR with anoxic phase decreased more than that of the MBR without anoxic phase.