NaClO based chemically enhanced backwash (CEB) is often administered to maintain membrane permeability during the operation of MBR. However, the effect and working mechanism of NaClO concentrations in CEB were rarely investigated. The current investigation examined the changes in membrane resistance, permeate production and membrane morphology with or without CEB in an anammox MBR to reveal the scrubbing effect of different NaClO concentrations (0-596 mg/L). Good cleaning effect indicated by membrane fouling rate of 1.98-2.26 kPa/day and membrane permeate production of 80-88 L was observed when NaClO concentration of 149-596 mg/L was used. The best cleaning effect was observed when 298 mg/L of NaClO was used. To explore the mechanism of CEB action, backwashing foulants were also analyzed. Insoluble EPS transformed into soluble forms like S-EPS or SMP after the sludge was exposed to NaClO. The NaClO based CEB removed 112-675 mg of polysaccharide (PS)/m2 in foulants at NaClO concentration of 149-596 mg/L, which was significantly higher than the value obtained by pure water (35 mg PS/m2). The possible mechanisms behind the detachment of soluble PS seemed as oxidation and sterilization by NaClO. The current investigation provides useful guidelines on NaClO concentrations applied during CEB for anammox MBR.