During the combined system operation period, the increase rates of Rt were 0.69 × 1012 m−1 d−1 for CANON MBR and 1.04 × 1012 m−1 d−1 for AnMBR. These values were much lower than those during the start-up stage, which suggested that biogas sparging was an effective approach to relieve membrane fouling by providing shear conditions. Additionally, the average fluxes obtained were 9.78 L/m2 h for AnMBR and 10.78 L/m2 h for CANON MBR with biogas sparging, which were close to the sustainable membrane flux of submerged AnMBR [35]. During the entire operational period, the number of membrane cleaning for AnMBR was much more than that for CANON MBR. Given this result with the increased rates of Rt and the average fluxes obtained in the two reactors, membrane fouling in AnMBR was much more severe compared with that in CANON MBR. Higher MLSS, OLR, residual COD and soluble microbial product production in AnMBR will cause more serious membrane fouling [10]. As a result, the cake layer formed in AnMBR might have relatively lower removability than that in CANON MBR because of the different sludge properties, although identical biogas flush was adopted in two reactors. In terms of inorganic fouling, struvite precipitation appeared to be one of the main inorganic foulants formed inorganic colloids and crystals on the membrane and pore surfaces [35]. In the present experiment, AnMBR may be more susceptible to inorganic fouling than CANON MBR because of the production of high ammonia and phosphate concentrations.