Gold nanorods have been recognized as a good candidate for developing novel nanomaterials due to their exceptional optical properties. However, their assemblies, especially with the assisted ionic liquid, have not been well characterized. In this paper, we report the self-assembly of gold nanorods using thiol-functionalized ionic liquid (1-methyl-3-(2'-mercaptoacetoxyethyl) imidazolium bromine) (TFIL). We found that gold nanorods can self-assemble via two different ways: From end-to-end to side-by-side with the increase of TFIL concentration. The shift of the absorption peak in UV-vis spectrum indicates the change of the assembly fashion. We propose that the pi-pi stacking interactions between the imidazole rings of TFIL molecules play the most important role in regulating the assembly process. The energy calculation further demonstrated that the face-face stacked orientation was the most stable geometry at high TFIL concentration, which supports the proposed mechanism. These gold nanorod assemblies were shown to yield the large SERS enhancements for Rhodamine 6G. (C) 2014 Elsevier B.V. All rights reserved.