Polymer:fullerene nanoparticles (NPs) offer two key advantages over bulk heterojunction (BHJ) films for organic photovoltaics (OPVs), water-processability and potentially superior morphological control. Once an optimal active layer morphology is reached, maintaining this morphology at OPV operating temperatures is key to the lifetime of a device. Here we study the morphology of the PDPP-TNT (poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]pyrrole-1,4-dione-alt-naphthalene}):PC71BM ([6,6]-phenyl C71 butyric acid methyl ester) NP system and then compare the thermal stability of NP and BHJ films to the common poly(3-hexylthiophene) (P3HT): phenyl C61 butyric acid methyl ester (PC61BM) system. We find that material T g plays a key role in the superior thermal stability of the PDPP-TNT:PC71BM system; whereas for the P3HT:PC61BM system, domain structure is critical.