The origins of vertical phase separation and their implication on the device efficiency of poly(3-hexylthiophene):[6,6]-phenyl C61-butyric acid methyl ester (P3HT:PCBM) based solar cells, with both regular and inverted structures, were investigated. We found that the light irradiation and the filtration processes during the device fabrications are two key steps that induce the vertical phase separation in the active layers. Upon light irradiation, the devices with inverted structures exhibit improved power conversion efficiency, whereas the regular devices show degradation. The inverted devices spun cast with filtered P3HT:PCBM solution also present a better improvement as compared to regular devices. X-ray and ultraviolet photoemission spectroscopies indicate that both illumination and filtration enhance the vertical phase separation of the blend film with additional PCBM segregated to the bottom interface.