In this study, we used simultaneous synchrotron grazing incidence X-ray scattering and diffraction to elucidate the overall morphologies of bulk heterojunction (BHJ) thin film (ca. 100 nm) solar cells containing phase-separated poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C 61-butyric acid methyl ester (PCBM) domains. Specifically, the dimensions and orientation of the P3HT crystallites and the sizes of the PCBM aggregates in BHJ thin films were determined. The appropriate PCBM aggregate size and density required for an optimum performance of the film in the photovoltaics device resulted in deteriorated ordering in the out-of-plane direction, but improved the in-plane packing of the P3HT lamellae. When the P3HT crystallites and PCBM aggregates had comparable domain sizes and number densities, the interpercolated networks for electron- and hole-transport were optimized in the film. This new understanding of the underlying mechanism of carrier mobility in BHJ thin films might be crucial in improving the efficiency of future solar cells.