Here we report the application of a conjugated copolymer based on thiophene and quinoxaline units, namely poly[2,3-bis-(3-octyloxyphenyl)quinoxaline-5,8-diyl-alt-thiophene-2,5-diyl] (TQ1), to nanoparticle organic photovoltaics (NP-OPVs). TQ1 exhibits more desirable material properties for NP-OPV fabrication and operation, particularly a high glass transition temperature (Tg) and amorphous nature, compared to the commonly applied semicrystalline polymer poly(3-hexylthiophene) (P3HT). This study reports the optimisation of TQ1:PC71BM (phenyl C71 butyric acid methyl ester) NP-OPV device performance by the application of mild thermal annealing treatments in the range of the Tg (sub-Tg and post-Tg), both in the active layer drying stage and post-cathode deposition annealing stage of device fabrication, and an in-depth study of the effect of these treatments on nanoparticle film morphology. In addition, we report a type of morphological evolution in nanoparticle films for OPV active layers that has not previously been observed, that of PC71BM nano-pathway formation between dispersed PC71BM-rich nanoparticle cores, which have the benefit of making the bulk film more conducive to charge percolation and extraction.