Organic solar cells (OSCs) with a bulk-heterojunction (BHJ) are promising energy conversion devices, because they are flexible and environmental-friendly, and can be fabricated by low-cost roll-to-roll process. Here, we systematically investigated the interrelations between photovoltaic properties and the domain morphology of the active layer in OSCs based on films of poly-(9,9-dioctylfluorene-co-bithiophene) (F8T2)/[6,6]-phenyl C71-butyric acid methyl ester (PC71BM) blend annealed at various temperatures (Tan). The scanning transmission X-ray microscopy (STXM) revealed that fullerene mixing (ΦFullerene) in the polymer matrix decreases with increase in Tan while the domain size (L) is nearly independent of Tan. The TEM-S mapping image suggests that the polymer matrix consist of polymer clusters of several nm and fullerene. We found that the charge formation efficiency (ΦCF), internal quantum efficiency (ΦIQ), and power conversion efficiency (PCE) are dominantly determined by ΦFullerene. We interpreted these observations in terms of the polymer clusters within the polymer matrix.