Ceramic membrane has emerged as a promising material to address the membrane fouling issue in membrane bioreactors (MBR). In order to optimize the structural property of ceramic membrane, four corundum ceramic membranes with the mean pore size of 0.50, 0.63, 0.80, and 1.02 μm were prepared, which were designated as C5, C7, C13, and C20, respectively. Long-term MBR experiments showed that the C7 membrane with medium pore size experienced the lowest trans-membrane pressure development rate. Both the decrease and increase of membrane pore size would lead to more severe membrane fouling in the MBR. It was also interesting that with the increase of membrane pore size, the relative proportion of cake layer resistance in total fouling resistance was gradually increased. The content of dissolved organic foulants (i.e., protein, polysaccharide and DOC) on the surface of C7 was quantified as the lowest among the different ceramic membranes. Microbial community analysis also revealed the C7 had a lower relative abundance of membrane fouling associated bacteria in its cake layer. The results clearly demonstrated that ceramic membrane fouling in MBR could be effectively alleviated through optimizing the membrane pore size, which was a key structural factor for preparation of ceramic membrane.