This experimental work investigated fouling characteristics induced by two different configurations of membrane bioreactor (MBR), which are submerged MBR and sidestream MBR with aerobic granular sludge. Submerged membrane bioreactor with granular sludge (Sub-MGSBR) ran the longest operation time 61 days with a steady overall TMP increase rate; Sidestream membrane bioreactor with granular sludge (SS-MGSBR) performed only 39 days, which exhibited Sub-MGSBR had more efficiently retarding membrane fouling. In both membrane bioreactors with flocculent sludge (MFSBRs) as a control, membrane foulants were compact, and cake resistance was the dominant fouling factor. In MGSBRs, however, pore blocking resistance turned out the key fouling factor. Especially in Sub-MGSBR, it went beyond 75%, and there was the most conglomeration of microorganisms of foulants with the highest porosity. Extracellular polymeric substances (EPS) content of foulants proved membrane fouling was hardly just for granules accumulation into cake but microorganisms’ growth in MGSBRs.