Polymer nanocomposites (PNCs), i.e., nanoparticle (NP) incorporated semiconducting polymers (SPs), constitute a class of active materials, where the dispersion and locations of the NPs and the crystallinity of the SPs play important roles in deciding their device performances. Herein Au nanoparticle (AuNP) mixed poly(3-hexylthiophene) [P3HT] was taken as a model PNC system and a unique combination of complementary techniques was utilized to address these dispersion-related structural issues, viz the organization and/or dispersion of AuNPs, its evolution with thermal annealing (TA) and their effects on the ordering or crystallization of the P3HT matrix. The layering of AuNPs near the interfaces, namely confined or near monolayer thick layer at the film-substrate interface and fluctuated or near bilayer thick layer at the film-air interface, are evident in the as-cast PNC thin films, indicating self-organization and phase separation tendencies of the similar and dissimilar materials (i.e., dominant decrease of enthalpic energy over entropy) and different (hard and soft) boundary conditions of the interfaces. On the other hand, appreciable dispersion of AuNPs inside P3HT matrix is evident after TA suggesting thermal energy induced diffusion of AuNPs through amorphous P3HT regions, overcoming the self-organization and phase separation (i.e., dominant increase of entropic energy over enthalpy). Such dispersion enhances the quantity (fraction or amount) and quality (planarity or conjugation length) of P3HT crystallites (and thus validates the dispersion of AuNPs in the amorphous P3HT regions) and their edge-on orientation and connectivity. This information or understanding is very useful for optimizing the structures of the PNC-based active layers for their better charge carrier mobility and device performances.