An important and integral effort toward understanding the formation and reorganization of mesoscale structures in functional organic thin films, being of fundamental importance to the development of tomorrow’s green energy technologies, is the continuous sharpening of the experimental analytical tools used to observe and quantify these structures. In this study we present a combined investigation of organic thin films by small-angle X-ray scattering (SAXS) and the relatively new technique of high-resolution phase-contrast ptychographic coherent X-ray diffraction imaging (CXDI). Using poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C₆₁-butyric acid methyl ester (PC₆₁BM) as a model system, we present the morphology development including phase separation in thermally annealed thin film blends. The state-of-the-art synchrotron SAXS measurements spanning a large q range from 2 × 10^–3 to 6 nm^–1 elucidate the multiscale structure within the material. Because the SAXS data in fact overlap with microscopy length scales, it is instructive to compare the small-q features of the SAXS patterns with corresponding images obtained by CXDI, as these techniques are based on the same physical interaction with the sample. While the technique of CXDI, here reaching a resolution of ∼100 nm, is currently too coarse to investigate the structural details at the length scale of the exciton diffusion lengths, the method proved consistent with the ultra-SAXS (USAXS) data and invaluable in resolving the thin-film dimensionality influence on the USAXS analysis. Our results not only offer a quantitative model for USAXS data analysis applied to thermally annealed thin films of P3HT/PC₆₁BM but also indicate the future applicability of emerging X-ray imaging techniques in retrieving the morphologies of low-contrast organic materials.