We developed a new method for characterizing molecular distribution in very thin liquid crystal layer (5-40nm) evaporated onto rubbed polyimide film used by grazing-incidence X-ray diffraction (GIXD). The diffraction peaks corresponding to intermolecular correlation perpendicular to longitudinal axis of liquid crystal molecule and the clear anisotropic distribution of liquid crystal molecules in a thin layer were successfully observed. We found that in the vicinity of the alignment film, the intermolecular spacing correlation perpendicular to longitudinal axis of the 5CB molecule was expanded by the alignment film, and that the ordering of the 5CB was not so high. As the distance from the alignment film the spacing came close to the intrinsic intermolecular spacing.