Quorum quenching (QQ) has been proved to be an efficient method to mitigate biofouling in membrane bioreactors (MBRs). In this paper, in order to enhance practicability of QQ microcapsules, we prepared three types microcapsules with same alginate cores (SAs). The microcapsules with polyacrylonitrile (PAN) layer showed excellent performance in preventing cell leakage from the microcapsules, increasing service life and improving mechanical strength. And confocal laser scanning microscopy images demonstrated that there were very little dead bacteria in the microcapsules with both chitosan and PAN layer than microcapsules with only PAN layer because chitosan layer can protect bacteria entrapped in cores from the hurt caused by poisonous PAN solution. At the same time, the microcapsules with PAN layer presented more efficient anti-biofouling ability in the physical washing test. At last, the bacterial microcapsules coated with both chitosan and PAN layer showed an obvious biofouling mitigation during the MBRs operation.