AbstractThe morphology of the active layer of a bulk heterojunction solar cell, made of a blend of an electron‐donating polymer and an electron‐accepting fullerene derivative, is known to play a determining role in device performance. Here, a combination of molecular dynamics simulations and long‐range corrected density functional theory calculations is used to elucidate the molecular‐scale effects that even minor structural changes to the polymer backbone can have on the “local” morphology; this study focuses on the extent of polymer–fullerene mixing, on their packing, and on the characteristics of the fullerene–fullerene connecting network in the mixed regions, aspects that are difficult to access experimentally. Three representative polymer donors are investigated: (i) poly[(5,6‐difluoro‐2,1,3‐benzothiadiazol‐4,7‐diyl)‐alt‐(3,3′″‐di(2‐octyldodecyl)‐2,2′;5′,2″;5″,2′″‐quaterthiophen‐5,5′″‐diyl)] (PffBT4T‐2OD); (ii) poly[(2,1,3‐benzothiadiazol‐4,7‐diyl)‐alt‐(3,3′″‐di(2‐octyldodecyl)‐2,2′;5′,2″;5″,2′″‐quaterthiophen‐5,5′″‐diyl)] (PBT4T‐2OD), where the fluorine atoms in the benzothiadiazole moieties of PffBT4T‐2OD are replaced with hydrogen atoms; and (iii) poly[(2,2′‐bithiophene)‐alt‐(4,7‐bis((2‐decyltetradecyl)thiophen‐2‐yl)‐5,6‐difluoro‐2‐propyl‐2H‐benzo[d][1,2,3]triazole)] (PT2‐FTAZ), where the sulfur atoms in the benzothiadiazole moieties of PffBT4T‐2OD are replaced with nitrogen atoms carrying a linear C3H7 side‐chain; these polymers are mixed with the phenyl‐C71‐butyric acid methyl ester (PC71BM) acceptor. This study also discusses the nature of the charge‐transfer electronic states appearing at the donor–acceptor interfaces, the electronic couplings relevant for the charge‐recombination process, and the electron‐transfer features between neighboring PC71BM molecules.