Uniformity, sensitivity, reproducibility, and cost are the critical parameters of practical surface-enhanced-Raman-spectroscopy (SERS) substrates. Herein, we proposed a High-Aspect-Ratio-Nano-Pillar-Array (HARNPA) substrate deposited silver by physical vapor deposition (PVD) methods (e.g. E-beam evaporation, sputtering, and a two-stage intermittent sputtering) to fabricate high-performance SERS substrates. The substrate by the E-beam evaporation has a significant SERS effect, but the Raman background induced by the exposure of the polymer HARNPA limits the analyte choice. The substrate by the sputtering method has better step coverage of silver but a lower enhancement factor. Therefore, we proposed a process of two-stage intermittent sputtering to solve these limitations. In addition, we define a factor called the signal-to-background peak ratio (S/B peak ratio) to evaluate the influence of the Raman background from the SERS substrate. Finally, we accomplished a SERS substrate with an S/B peak ratio of 3.48 by intermittent sputtering, which has the best linearity (R2 = 0.97) of the melamine concentration curve and the lowest detection limit (LoD = 5.6 × 10-7 M) that meets the regulatory requirements for melamine detection (3.96 × 10-6 M). The benefits of our SERS substrates are easy fabrication, high sensitivity (EF = 1.44 × 107), high reproducibility (CV = 8.4 %), and excellent uniformity (CV = 7 % in 4″ area), which are beneficial for mass production in the future.