Polymers with a perylenediimide (PDI) side chain (PAc12PDI) consist of two kinds of crystalline structures with various types of orientations in a thin film. Understanding the population of the microcrystalline structure and its orientation along the thickness is strongly desired. Grazing-incidence wide-angle X-ray diffraction (GIWAXD) measurements with hard X-rays, which are generally chosen as λ = 0.1 nm, are a powerful tool to evaluate the molecular aggregation structure in thin films. A depth-resolved analysis for the outermost surface of the polymeric materials using conventional GIWAXD measurements, however, has limitations on depth resolution because the X-ray penetration depth dramatically increases above the critical angle. Meanwhile, tender X-rays (λ = 0.5 nm) have the potential advantage that the penetration depth gradually increases above the critical angle, leading to precise characterization for the population of crystallite distribution along the thickness. The population of the microcrystalline states in the PAc12PDI thin film was precisely characterized utilizing GIWAXD measurements using tender X-rays. The outermost surface of the PAc12PDI thin film is occupied by a monoclinic lattice with a = 2.38 nm, b = 0.74 nm, c = 5.98 nm, and β = 108.13°, while maintaining the c-axis perpendicular to the substrate surface. Additionally, the presence of solid substrate controls the formation of the crystallite with unidirectional orientation.