A study was conducted to demonstrate the application of grazing incidence small-angle X-ray scattering (GISAXS) and wide-angle X-ray diffraction (GIWAXD) to study the morphology of poly(3-hexylthiophene)/[6,6]-phenyl-C 61-butyric acid methyl ester (P3HT/PCBM) bulk heterojunction solar cells after their thermal annealing. This approach allowed to investigate the effects of the sizes of the PCBM clusters and p3HT crystallites on the power conversion efficiencies of bulk heterojunction solar cells. The study indicated that the strength of substrate interactions on a polymer thin films was minimum when the film thickness is more than 17 nm, judging from the glass transition temperature. It appears that improved power conversion efficiently requires the value of Rg of the PCBM clusters to be greater than 20nm and the value of D100 of the P3HT crystallites to be greater than 16nm for an active layer thickness of ca. 100nm.