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Here, we report an efficient approach to optimize the performance of surface enhanced Raman scattering (SERS) substrate. The geometry of the SERS substrate consists of the Au film deposited on polymer grating. Firstly, an optimized value of grating geometries and Au thickness has been performed by rigorous-coupled wave analysis (RCWA).The SERS substrate were fabricated by the laser interference lithography (LIL) and magnetron sputtering of Au thin films. The effect of the Au thin film prepared by magnetron sputtering at different deposition time (5-180 s) and operated pressure (3-5 mTorr) on the SERS performance were investigated and compared with the RCWA simulation results. The morphology of the obtained samples was observed by field-emission scanning electron microscopy (FE-SEM). The results indicated that optimal SERS substrate with deposition time of 180 s and 3 mTorr-operated pressure was obtained. The limit of detection for methylene blue (MB) and methyl parathinon were evaluated at 10^(-4) M and 10^(-2) M, respectively. Moreover, our SERS substrate shows the application of a portable Raman spectrophotometer which also promising for on-site pesticide substance detection.