The local structure of highly ordered mesostructured silica films was investigated by using a synchrotron X-ray microbeam and a CCD X-ray detector. Two-dimensional X-ray diffraction patterns clearly showed the detailed arrangement of the mesostructures, in which the hexagonal mesochannels aligned uniaxially in the mesostructured silica films formed on a silica glass substrate with a rubbing-treated thin polyimide coating. The alignment direction was shown to be perpendicular to the rubbing direction. The grazing incidence condition revealed the structural anisotropy of the mesostructures, while normal incidence X-ray diffraction data indicated the in-plane structural uniformity of the films. Extra spots were observed in the diffraction patterns. This suggested that the X-ray beam reflected at the boundary of the mesostructured silica film and the substrate.