We develop a solvent-assisted room temperature nanoimprint lithography (SART-NIL) technique to fabricate an ideal active layer consisting of poly(3-hexylthiophene) nanopillar arrays surrounded by [6,6]-phenyl-C61-butyric acid methyl ester. Characterization by scanning electron microscopy, two-dimensional grazing incidence wide angle X-rays diffraction, and conducting atomic force microscopy reveals that the SART-NIL technique can precisely control the size of P3HT nanopillar arrays. With the decrease in diameters of P3HT nanopillar arrays, the P3HT nanopillar arrays exhibit a more preferable face-on molecular orientation, enhanced UV-vis absorption and higher conducting ability along the direction perpendicular to the substrate. The ordered bulk heterojunction film consisting of P3HT nanopillar arrays with a diameter of ∼45 nm (OBHJ-45) gives face-on orientation, a high interfacial area of 2.87, a high conducting ability of ∼130 pA and efficient exciton diffusion and dissociation. The polymer solar cell (PSC) based on an OBHJ-45 film exhibits a significantly improved device performance compared with those of PSCs based on the P3HT nanoapillar arrays with diameters ∼100 nm and ∼60 nm. We believe that the SART-NIL technique is a powerful tool for fabricating an ideal active layer for high performance PSCs.