The present invention provides a method for an organic thin film solar cell and an organic thin film solar cell manufactured by the same, which can reduce manufacturing cost by simplifying manufacturing process, ensure long-lasting durability and stability, and improve energy conversion efficiency of the solar cell. In certain preferred aspects, the present invention provides a method for manufacturing an organic thin film solar cell by ion beam treatment, the method including: forming a nanopattern having a concavo-convex structure by irradiating an ion beam onto the surface of a flexible plastic film substrate; and sequentially stacking a bottom electrode layer, a photoactive layer for photoelectric conversion, and a top electrode layer, which have a nanoscale thickness, on the nanopattern of the substrate such that an electron donor and an electron acceptor in the photoactive layer, where electrons and holes are separated, form a nanopattern by the concavo-convex structure of the substrate, thus forming a bulk heterojunction structure.