A multi-layer nanogap array composed of three linearly aligned gold nanogaps is fabricated for a surface-enhanced Raman spectroscopy (SERS) substrate. The overall process for the proposed structure is simple and reliable with the use of a photolithography-free fabrication process, which includes only deposition and etching. Chemical vapor deposition (CVD) is employed to form a uniform and highly controllable nanogap array. The nanogap width, a crucial parameter in SERS, is determined by the sacrificial film thickness of CVD. Experiments on nanogap width and polarization angle dependence are carried out to characterize the fabricated multi-layer nanogap array as an SERS substrate.