We demonstrate here that the nanostructure of poly(3-hexylthiophene) and [6,6]-phenyl-C61-butyric acid methyl ester (P3HT/PCBM) bulk heterojunction (BHJ) can be tuned by inorganic nanoparticles (INPs) for enhanced solar cell performance. The self-organized nanostructural evolution of P3HT/PCBM/INPs thin films was investigated by using simultaneous grazing-incidence small-angle X-ray scattering (GISAXS) and grazing-incidence wide-angle X-ray scattering (GIWAXS) technique. Including INPs into P3HT/PCBM leads to (1) diffusion of PCBM molecules into aggregated PCBM clusters and (2) formation of interpenetrating networks that contain INPs which interact with amorphous P3HT polymer chains that are intercalated with PCBM molecules. Both of the nanostructures provide efficient pathways for free electron transport. The distinctive INP-tuned nanostructures are thermally stable and exhibit significantly enhanced electron mobility, external quantum efficiency, and photovoltaic device performance. These gains over conventional P3HT/PCBM directly result from newly demonstrated nanostructure. This work provides an attractive strategy for manipulating the phase-separated BHJ layers and also increases insight into nanostructural evolution when INPs are incorporated into BHJs.