Ceramic membrane plays an important role in separation process with advantages of high thermal and chemical resistances, but its applications on the nanofiltration are restricted because of the limitation of pore size. In this study, a commercial tubular ceramic membrane with pore diameter of 0.1 μm was firstly coated with mesoporous silica substrates, in which ZIF-67 nanocrystals were generated layer-by-layer inside the mesochannels via liquid phase epitaxy growth method. The open pore size of ceramic membrane can be precisely controlled by increasing the growth cycles of ZIF-67 nanocrystals. The influence of preparation conditions on the dye separation was investigated, including growth cycles, precursor concentration, and molar ratio of Co2+/2-methylimidazole (Co2+/Hmim). Under the optimized conditions, the rejection of methylene blue, methyl orange, chromium black T, rhodamine B, acid fuchsin, and Congo red were in the range of 92–99 % with membrane fluxes of 0.45–0.73 L m−2 h−1. Bovine serum albumin solution was used to evaluate the anti-fouling abilities of the ceramic membrane. The flux recovery ratio, which was calculated according to the ratio between the water permeance after washing and before filtration, was 52.3 % with the flux decline rate of 66.3 %.