In this study, the effects of submerged microfiltration process operation methods on membrane separation characteristics were investigated to minimize the membrane contamination. The experimental setup for two MBR systems, one with anoxic phase (MBR(A/O/A)) and the other without anoxic pahse (MBR(-/O/_)). When MBR(A/O/A) process operation cycle 6~12 h/cycle, the contamination of membrane was decreased while the operation period was extended. The nitrogen removal efficiencies of 6, 8, 12 h/cycle were 50%, 67%, 88%, respectively and the phosphorous removal efficiencies of each h/cycle were 36.8%, 47%, 65.4%, respectively. The organics removal efficiency was over 90% for all operation cycles. According, it is considered that the MBR(A/O/A) process developed in this study can be used very efficiency as small scale water recycle system for removing organics and nutrients simultaneously.