Surface enhanced Raman scattering (SERS) is a highly sensitive spectroscopy technique, which is widely used in chemical reaction detecting, medical diagnostics, and food analysis. The construction of the substrate structure has a very important influence on enhancing the SERS signal of the probe molecule. In this paper, a three-dimensional (3D) pyramid stereo composite SERS substrate is prepared by using polymethyl methacrylate (PMMA) to encapsulate silver nanoparticles, which achieves high sensitivity detection of Rhodamine 6G (R6G) molecules. By adjusting the dispersion density of silver nanoparticles in the PMMA acetone solution, the effective oscillation of light in the pyramid valley is realized, which not only ensures the high-density "hot spot" effect of the 3D structure, but also avoids deforming the adsorption probe molecules caused by the metal-molecule interaction. It also effectively prevents the silver nanoparticles from being oxidized and provides a larger range of electromagnetic enhancement for probe molecules, resulting in a stable output of the enhanced Raman signal. This research result provides an effective strategy for designing a high performance and reusable SERS substrate, meanwhile, it has important guiding significance for further designing an SERS substrate with improved 3D structure in the future study.