Mullite whiskers have been successfully grown on the surface of cordierite honeycomb ceramics by the gas-phase growth method. The cilia-like structure can significantly improve the filtration precision. The acicular mullite whiskers grew on the cordierite present nanometer-sized (200–300 nm) diameters and micrometer-sized (1–2 μm) lengths. Owing to mullite whiskers growth on surface of pores, the morphology of pores is changed and the microstructure change will lead to filtration precision increasing. The composites with the largest ratio of length/diameter mullite whiskers possess the highest filtration precision, which can reach 122.42 nm, 255.00 nm and 458.67 nm in intercepting different particle size of nano-SiO2, respectively. Moreover, the bending strength of the cordierites were enhanced due to the generation of mullite whiskers, these generated whiskers intersected with each other forming many unfixed lap-jointing points. The porous ceramics membrane with the unique microstructure has great potential application in gas-solid separation field and liquid-solid separation field.