Membrane fouling, the key disadvantage that inevitably occurs continuously in the membrane bioreactor (MBR), baffles the wide-scale application of MBR. Ceramic membrane, which possesses high chemical and thermal resistance, has seldom been used in MBR to treat municipal wastewater. Four ceramic membranes with the same materials but different pore sizes, ranging from 80 to 300 nm, were studied in parallel using four lab-scale submerged MBRs (i.e., one type of ceramic membrane in one MBR). Total COD and ammonia nitrogen removal efficiencies were observed to be consistently above 94.5 and 98%, respectively, in all submerged ceramic membrane bioreactors. The experimental results showed that fouling was mainly affected by membrane’s microstructure, surface roughness and pore sizes. Ceramic membrane with the roughest surface and biggest pore size (300 nm) had the highest fouling potential with respect to the TMP profile. The 80 nm membrane with a smoother surface and relatively uniform smaller pore openings experienced least membrane fouling with respect to TMP increase. The effects of the molecular weight distribution, particle size distribution and other biomass characteristics such as extracellular polymeric substances, zeta potential and capillary suction time, were also investigated in this study. Results showed that no significant differences of these attributes were observed. These observations indicate that the membrane surface properties are the dominant factors leading to different fouling potential in this study.