This study comprehensively explores the nanostructural properties of two diketopyrrolo[3,4-c]pyrrole-1,4-dione (DPP)-based small molecules with different alkyl side groups and their blends with the fullerene derivative PC₇₁BM, using grazing-incidence wide-angle X-ray scattering synchrotron techniques. Preferentially relative face-on orientation within the larger and more ordered stacking phase of SM1 with its shorter side group (ethylhexyl) was observed in the majority of both pristine and blend thin films, whereas SM2 crystals showed strictly perpendicular orientation. These contrasting crystalline characteristics led to significant differences in the results, from which crystalline structure–performance property correlations are proposed. Thus, the results not only demonstrate important scientific insights into the relationship between molecular structure and crystalline formation but also provide molecular design directions that will facilitate further improvement to the morphology and performance of DPP-based small-molecule solar cells.