In bulk-heterojunction solar cells, device performance is influenced by both the intrinsic properties of the individual components - typically conjugated polymers and fullerene derivatives - and how they assemble and interact at their interface. The ability of fullerene to intercalate within the side-chains of a conjugated polymer can significantly affect the microstructure and overall device performance. Here, a series of computational chemistry approaches are applied to investigate the relationships between structure and property in intercalated polymer:fullerene blend. Using a combination of molecular mechanics (MM) calculation and simulations of 2D grazing incidence X-ray diffraction (GIXD) patterns, we have determined the molecular packing configuration of poly (2,5-bis (3-tetradecyl thiophene-2-yl) thieno[3,2-b]thiophene) (PBTTT-C₁₄) and a blend of PBTTT-C₁₄ and [6,6]-phenyl-C₇₁-butyric acid methyl ester (PC₇₁BM). Based on the confirmed packing structures, the electronic properties and morphological disorder were examined using density functional theory (DFT) and molecular dynamics (MD) calculations, respectively; we also investigated the intermolecular interaction energies behind the structure formation. Finally, we examined the vibrational, redox, and optical properties of the pristine polymer and a series of fullerene derivatives to understand the characteristic modes related to the various charged states of the systems.