We report detailed analysis of the thin film morphology (molecular packing, molecular conformational order, and vertical phase separation) – performance (charge transport, photocurrent generation, and photovoltaic performance) relationships under nanowire formation and subsequent thermal annealing in polymer:fullerene blends. Nanowires of poly(3-hexylthiophene) (P3HT) are formed by controlled precipitation from solution and blended with [6,6]-phenyl-C₆₁-butyric acid methyl ester (PCBM) to form bulk heterojunction thin films. The formation of nanowires and further thermal annealing result in increased molecular order of the P3HT, where the short-range conformational order is maximised by annealing at 100 °C and decreases when annealed at higher temperatures, but the quality of long-range molecular packing and lamellar packing distance increase with annealing temperature up to 150 °C. The long-range order correlates strongly with an increase in hole mobility, but the reduction in short-range conformational order indicates a slight reduction in planarity of the conjugated backbone in this aggregated polymer morphology. Photoconductive atomic force microscopy reveals enhanced connectivity of the hole transporting nanowire network as a result of thermal annealing. Additionally, we find that the nanowire morphology results in a favourable vertical phase separation, with PCBM enrichment at the electron-extracting surface in the conventional architecture, which is contrary to the non-nanowire case. This effect is further encouraged by thermal annealing, resulting in an enhancement of open-circuit voltage, and represents a morphological advantage over conventional P3HT:PCBM devices. Our study identifies an important interplay between long-range and short-range molecular order in charge generation, transport, extraction, and hence solar cell device performance.