Changes in the nanoscale morphologies of the blend films of poly (3-hexylthiophene) (P3HT) and [6,6]-phenyl-C-61-butyric acid methyl ester (PCBM), for high-performance bulk-heterojunction (BHJ) solar cells, are compared and investigated for two annealing treatments with different morphology evolution time scales, having special consideration for the diffusion and aggregation of PCBM molecules. An annealing condition with relatively fast diffusion and aggregation of the PCBM molecules during P3HT crystallization results in poor BHJ morphology because of prevention of the formation of the more elongated P3HT crystals. However, an annealing condition, accelerating PCBM diffusion after the formation of a well-ordered morphology, results in a relatively stable morphology with less destruction of crystalline P3HT. Based on these results, an effective strategy for determining an optimized annealing treatment is suggested that considers the effect of relative kinetics on the crystallization of the components for a blend film with a new BHJ materials pair, upon which BHJ solar cells are based.