A novel method with high flexibility and efficiency for developing SERS substrates is proposed by patterning nanostructures on Si substrates using focused ion beam direct writing (FIBDW) technology following with precise thermal evaporation of gold film on the substrate. The effect of SERS on the substrate was systematically investigated by optimizing the processing parameters and the gold film thickness. The results proved that small dwell time could improve the machining accuracy and obtain smaller nanogap. The Raman-enhanced performance of the substrate was investigated with 10-6mol/L Rhodamine 6 G solution. It was indicated that the elliptic nanostructures with 15-nm spacing on Si substrates, coated with approximately 15-nm thick gold film, have exhibited a high-enhanced performance, but dramatic performance degradation was found as the gold film thickness further increased, which most probably resulted from changes of the nanostructures' morphology such as elliptical tip and spacing. To avoid the morphological changes effectively after depositing gold film, optimization design of the nanostructures for FIBDW on Si substrates was proposed. Besides, a similar phenomenon was found when the gold film was less than 15nm because there was little gold remaining on the substrate. The method proposed in this paper shows a great potential for the higher performance SERS substrates development, which can further reduce the spacing between hot spots.