Synthesis of metal nanostructures arrays with large amounts of small nano-gaps on a homogenous macroscale is of significant interest and importance in chemistry, biotechnology, physics, and nanotechnology because of their enhanced properties. However, the fabrication of uncovered nano-gaps with high-density and uniformity is rather difficult due to the complex and multiple synthetic steps. In this research, a facile and low-cost approach is demonstrated for the synthesis of high-density small nano-gaps (about 3.4 nm) between silver nanostructure array patterns (SNAPs) over a large area. Uniform nano-hole patterns were periodically generated over an entire substrate using nano-imprint lithography. Electrochemical reaction at the high over-potential produced multiple silver nanocrystals inside the nano-hole patterns, generating a high-density of small and uncovered nano-gaps. Finally, we fully demonstrate their application in the rapid detection of rhodamine 6G (R6G) molecules by surface-enhanced Raman scattering (SERS) spectroscopy with a very low detection limit (1 fM) as well as excellent signal uniformity (RSD < 8.0% ± 2.5%), indicating an extraordinary capability for single-molecule detection.