Nanoimprinting lithography (NIL) is investigated as a promising method to define nanostructure; however, finding a practical method to achieve large area patterning of conjugated polymer remains a challenge. We demonstrate here that a simple and cost-effective technique is proposed to fabricate the nanoimprinted P3HT nanograting by solvent-assisted room temperature NIL (SART-NIL) method with patterned ETFE film as mold. The patterned ETFE template is produced by embossing ETFE film into a patterned silicon master and is used as template to transfer nanogratings during the SART-NIL process. It indicates that highly reproducible and well-controlled P3HT nanograting film is obtained successfully with feature size of nanogratings ranging from 130 to 700 nm, due to the flexibility, stiffness, and low surface energy of ETFE mold. Moreover, the SART-NIL method using ETFE mold is able to fabricate nanogratings but not to induce the change of molecular orientation within conjugated polymer. The conducting ability of P3HT nanograting in the vertical direction is also not damaged after patterning. Finally, we further apply P3HT nanograting for the fabrication of active layer of OBHJ solar cell device, to investigate the morphology role presented by ETFE mold in device performance. The device performance of OBHJ solar cell is preferential to that of PBHJ device obviously.Electronic supplementary materialThe online version of this article (doi:10.1186/s11671-016-1481-y) contains supplementary material, which is available to authorized users.