A novel nanoporous mat structure was made of gold nanoparticles through a simple, inexpensive self-assembly process as a bottom-up approach to produce an affordable and high-quality SERS substrate. This nanostructure mat shows an excellent SERS reproducibility, physical stability, and strong Raman enhancement, which may satisfy all the criteria as a universal-type SERS substrate. The limit of detection for crystal violet dye on the nanostructured substrates is estimated to reach ppb levels and the SERS enhancement factor is found to be two orders of magnitude higher than that from conventional de-alloy nanoporous films. Mechanical strength of the nano-cluster network can be increased by a post-assembly annealing process. The nanoparticle-based SERS substrate holds promise in practical sensing applications toward a rapid determination of harmful substances or contaminants in food and environment.