All the time, SERS based metal nanoparticles structure prepared by vacuum thermal evaporation and high-temperature annealing has been widely used in various detection fields due to its good sensitivity, stability and uniformity. Because of its excellent optical properties, chemical inertness and fluorescence quenching effect, graphene has been a hot material in optical micro-nano devices since its discovery. Graphene can also effectively separate probe molecules and substrate to optimize Raman spectral quality, so it has been widely used in the SERS research field. Meanwhile, graphene can effectively isolate the direct contact between the metal nanostructure and the air to prevent the metal nanostructure from being oxidized and become ineffective. It can also catalyze the deoxidation reaction of silver oxide to improve the stability of SERS substrate. Affected by the types and thickness of the metal film, annealing time, temperature and pressure, and the type of gas during the preparation process of the graphene/metal nanostructure SERS substrate, the influence on metal nanostructure morphology is quite different. Besides, the Raman spectra of graphene will be enhanced, frequency-shifted and broaden because of the stress and doping characteristics of the Raman peak. (1) In this paper, the SERS substrate of graphene/silver nanocomposite structure was prepared by vacuum thermal evaporation and high-temperature annealing, the forming mechanism model of metal nanoparticles was established, and the forming process of metal nanoparticles was analyzed from the three stages of hole formation, hole growth and metal island formation. The silver films at 5, 10, 15 and 20 nm were deposited, and the coverage rates of silver nanoparticles after annealing were ~35.1%, ~24.4%, ~30% and ~96.0%, respectively. Graphene was transferred on the silver film samples, after annealing treatment, it was found that graphene prevented the formation of silver nanoislands. (2) The influence of the thickness of the silver film, the effect of covered graphene cover on the geometric morphology, and Raman enhancement characteristics of the composite structure was theoretically analyzed. Due to its high Young’s modulus and surface tension, graphene could effectively inhibit the transformation of the silver film to nanoparticles in the annealing process so as to realize the regulation of the surface morphology of the composite structure. (3)The effect of silver nanoparticle structure on Raman spectrum of graphene was studied experimentally, and the reasons for the effect of different silver film thickness on Raman spectrum enhancement, shift and broaden of graphene were analyzed theoretically.