Crystallographic orientation of mesostructured silica films on a substrate drastically changes when the substrate is modified with an anisotropic surface. The < 01 > axis of a two-dimensional (2D) hexagonal structure of the film prepared on a polyimide surface using C22EO20 as a structure-directing agent changes from perpendicular to parallel with respect to the substrate after a rubbing treatment of polyimide, which is accompanied by the simultaneous unidirectional alignment of the cylindrical pores in the plane of the film. The normal direction of the film is < 2 (1) over bar >, which has never been observed in the mesostructured silica films reported so far including those with controlled in-plane alignment of the mesochannels. The change of the orientation with respect to the substrate can be explained by the increased lateral distance between the adjacent surface micelles, which is caused by the elongation of the alkyl chains of the surfactant molecules induced by the adsorption onto the polymer surface with a molecular-level anisotropy. These results show that the total structural orientation of the mesostructured silica film is determined by the matching of the intrinsic lattice constant of the mesostructured silica with that of the surface micelle structure on a substrate.