To better understand the physics of the photoactive layer in the organic photovoltaic devices, it is necessary to gain a quantitative understanding of the morphology and the manner in which it develops. A key element in the kinetics associated with the structure development is the interdiffusion of the components. To that end we used P3HT/PCBM bilayers as a model to investigate the interdiffusion of the components and its role in the development of the morphology. A detailed description of the diffusion behavior and the morphology developed from a layer of P3HT in contact with a layer of PCBM during thermal annealing is given. Amorphous P3HT and PCBM are shown to be highly miscible and PCBM can penetrate into the P3HT layer through the P3HT amorphous region and form the bulk heterojunction structure within a few seconds of annealing at 150 °C. The results indicated that one phase is an ordered P3HT domain and the other phase is the mixture of amorphous P3HT and PCBM which is not consistent with a phase separation of the components by a spinodal decomposition mechanism.