The performance effect of organic solar cells with subphthalocyanine (SubPC)/fullerene (C60) bilayer was investigated with thermal treatment while changing the vacuum deposition rate of SubPC. The thermal annealing at 100 degrees C increases the optical absorption intensity of SubPC film at the spectral range of 550-630 nm. The X-ray diffraction (XRD) patterns indicates that the thermally annealed film formed the much-ordered morphology, as compared to the non-annealed film. Consequently, thermally treated solar cell exhibited almost 10% higher power conversion efficiency (PCE) compared to the non-annealed device. The fill factor (FF) and PCE of the devices were increased as the deposition rate of SubPC was increased up to 5 A/s and then saturated at higher deposition rates (> 5 A/s). The surface roughness of SubPC films, measured with an atomic force microscope, increased from 1.1 to 5 nm as the deposition rate increased from 1 to 7 A/s. These results imply that rough surface increases the interfacial area between SubPC and C60 and thereby improves the separation of photogenerated electron and hole pairs at the SubPC/C60 interface.