A modified method was used for cell entrapped beads (CEBs) preparation and two aeration intensities (low and high aeration intensity) was supplied as factors to investigate the change of quorum quenching performance for membrane biofouling in membrane bioreactor (MBR). Dehydrogenase activity and growth trend of activated sludge were improved at high aeration intensity. Compared with C-MBR (with vacant beads), QQ-MBR (with CEBs) had more stable quorum quenching activity and longer application time at high aeration intensity, in which the proteins and polysaccharides were reduced by 15 and 20%, respectively. The difference of EPS concentration in mixed liquor was attributed to the protein concentration controlled by quorum quenching bacteria, meanwhile sufficient organics was necessary to maintain the process. The better settleability, greater stability and relatively lower hydrophobicity of activated sludge properties was achieved with quorum quenching. The scouring effect of CEBs was promoted at high aeration intensity, further controlling the membrane biofouling.