It has been proved that surfactant-silicate supramolecular architecture formed on a silicon substrate is strongly affected by the crystal orientation of a silicon wafer, indicating the variation of the interactions between the surfactants and the silicon surfaces. The hexagonal mesoporous silica film with aligned mesochannels was grown on a (110) wafer, whereas the mesochannels were not aligned in the films grown on (100) and (111) wafers. The alignment direction of the mesochannels on the (110) wafer is parallel to the [001] direction. The Gaussian distribution of the alignment direction with a full width at half-maximum (fwhm) of 29 degrees was shown by in-plane X-ray diffraction. The hexagonal packing of the mesochannels in the film is distorted. The strong anisotropy of the atomic arrangement of silicon on the (110) surface causes the preferential alignment of mesochannels.