Mixtures of polythiophene and fullerene are intensely studied for organic photovoltaic applications. Control of nanoscale morphology of these materials is critical for device performance, but characterization and understanding of this morphology and how it arises is lacking. We use energy-filtered transmission electron microscopy (EFTEM) to obtain high-contrast images of P3HT nanocrystals in organic semiconductor mixtures. Grazing-incidence small-angle X-ray scattering correlates well with the length scales obtained from EFTEM images; we combine the two techniques to follow the morphology evolution under different material processing histories. EFTEM also measures local P3HT concentration in PCBM-rich regions, proving that these components are partially miscible. We determine the P3HT-PCBM X parameter and Flory-Huggins phase diagram, which predicts miscibility for P3HT volume fractions above 0.42. This miscibility suppresses fullerene crystallization. The nanoscale morphology in these materials, critical for solar cell performance, is driven by P3HT crystallization from a partially miscible blend. © 2011 American Chemical Society.