In this study, the three-dimensional (3D) nanoscale organization in the photoactive layers of poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM) is revealed by electron tomography. Morphologies suggested by previous experimental evidence were, for the first time, observed directly with a nanometer resolution and studied in detail. After annealing treatment, either at elevated temperature or during slow solvent evaporation, genuine 3D nanoscale networks are formed with high crystalline order and favorable concentration gradients of both P3HT and PCBM through the thickness of the photoactive layer. These favorable morphological changes account for a considerable increase of the power conversion efficiency in corresponding solar cell devices.