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A desirable vertical phase separation of a bulk-heterojunction was achieved by inserting a P3HT layer between the blend layer and the poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS) layer. According to the high (PEDOT:PSS) and low (P3HT) surface energies of substrate, it might be possible to modulate the vertical phase separation in the bulk-heterojunction. The result of vertical phase separation was determined using time-of-flight secondary-ion mass spectroscopy analysis. A controlled thickness of 50 nm for the inserted P3HT layer prevented undesirable light absorption and the power conversion efficiency of this condition was increased by 44% compared to that of a reference device.