The composite structure of metal nanoparticle and metal film can be used as a surface-enhanced Raman scattering (SERS) substrate to significantly enhance the Raman signal of adsorbed molecules due to the strong coupling between local surface plasmons and propagating surface plasmons. An SERS substrate of the composite structure with gold nano-cubes and gold film separated by polymethylmethacrylate (PMMA) film is proposed. The optimum thickness of PMMA is 15 nm obtained by numerical simulation through using finite element method. The composite structure of PMMA spacer with a thickness of 14 nm is prepared experimentally. Using R6G as the Raman probe molecules and He-Ne laser with a wavelength of 633 nm as an excitation source, the SERS effect of the composite structure and single gold nano-cubes are studied. It is found that the composite structure can make the probe molecules produce a stronger Raman signal than the single structure. Furthermore, the SERS spectra of R6G molecules on the composite structure under the condition of aqueous solution of gold nano-cubes with different concentrations are studied. The results show that when the concentration of gold nano-cubes’ aqueous solution is 5.625 ${\text{μ}}{\rm g/mL}$, the SERS signal of the R6G molecules on the composite structure is strongest. The lowest concentration of R6G molecules which can be detected is about 10^–11 mol/L.