Surface enhanced Raman scattering (SERS) has attracted great attention of scientists in the last few decades due to its wide range of applications, especially in detecting chemical compounds even at single molecular level. In this research, we combine sputtering and post annealing method to prepare gold nanoparticles with uniform distribution on cover glass substrates, which work as efficient SERS substrates. This work studies the effect of gold thickness on the formation of nanoparticles during annealing process. The effect of size, inter-distance and morphology of gold NPs on plasmon properties was studied by scanning electron microscope and absorption spectroscopy. The enhancement capability of different morphologies was also verified by using Finite Different Time Domain (FDTD) technique. The as-prepared gold nanoparticles arrays are efficient surface enhanced Raman scattering substrates as demonstrated by the ability to detect methylene blue at concentration as low as 10−10 M. The facile, cost-effective fabrication process is convenient to scale up for mass production of high sensitivity surface enhanced Raman substrates.