This manuscript reports the mixing behavior, interdiffusion, and depth profile of 1-[3-(methoxycarbonyl)propyl]-1-phenyl-[6,6]C61 (PCBM):low-bandgap (LBG) polymer thin films that are formed by thermally annealing initial bilayers. The extent of mixing of PCBM is higher in polymers that include the 2,1,3-benzothiadiazole (BT) unit than in polymers that incorporate the 2,1,3-benzooxadiazole (BO) unit. This difference is ascribed to the enhanced mixing behavior of PCBM with the benzothiadiazole functionality than with benzooxadiazole functionality, which is attributed to preferred intermolecular interactions. The increased polymer/fullerene mixing is found to be crucial for optimal device performance. A decrease of polymer/fullerene mixing reduces the donor/acceptor interface, which lowers the probability of exciton dissociation and charge generation. Moreover, low PCBM mixing provides limited pathways for electron transport out of a miscible region, due to long distances between adjacent PCBM in such a miscible phase. This inhibits electron transport and increases the recombination of free charge carriers, resulting in a decrease in short circuit current and device performance. These results further exemplify the importance of the thermodynamic mixing behavior of the polymer:fullerene pair in designing next-generation conjugated polymers for organic photovoltaic (OPV) applications, as this controls the final morphology of the OPV active layer.