The invention relates to a surface enhanced raman scattering substrate and a preparation method thereof. The surface enhanced raman scattering substrate comprises a spherical empty shell and a film, wherein the film covers an upper half spherical surface of the spherical empty shell to form a composite micro-cavity structure, the spherical empty shell is the empty shell of any one of ZnO, TiO2, Al2O3, GaN and Al, and the film is an Ag film or an Au film. The preparation method of the substrate comprises the following steps: self-assembling an array template, adjusting the array template, depositing any one of ZnO, TiO2, Al2O3, GaN and Al on the array template, annealing the template in a nitrogen atmosphere, and depositing the Ag film or the Au film on the annealed array template. The multi-polar mode of the composite micro-cavity structure is coupled with a resonance mechanism, so that the advantages of simplicity in operation, rapidness in detection and high sensitivity can be realized, and the application prospect in the fields such as food security, stimulant detection and the like is wide.