The effects of thermal annealing on the efficiency of heterojunction photovoltaic (PV) cells that were fabricated using poly(3-hexylthiophene) (P3HT) and methanofullerene, [6,6]-phenyl C61-butyric acid methyl ester (PCBM) were investigated. The absorption spectra showed that the absorption intensity of the P3HT:PCBM layer that was annealed for 5 min had the highest value among the several samples with different annealing temperatures. The atomic force microscopy image showed that the P3HT:PCBM layer that was annealed for 5 min had the best surface morphology. The X-ray photoelectron spectroscopy demonstrated that the P3HT:PCBM layer that was annealed at 140 degrees C for 10 min enhanced the PCBM aggregation on the surface Al layer that was covered by the P3HT:PCBM layer. The efficiencies of the PV cells that were annealed at 3, 5, and 10 min were approximately 2.7, 4.2, and 3.5%, respectively. Based on the experiment results, the variations in the efficiency of the PV cells due their thermal treatment were described.