To intuitive and accurate quantitatively analyze Raman enhancement of surface enhanced Raman scattering substrate structure, three-dimensional composite structure of silver nanoparticles modified vertically aligned carbon nanotube array is produced by magnetron sputtering and thermal annealing process; Relevant experiments using Rhodamine 6G (R6G) solution as the molecular probes are conducted to analyze surface enhanced Raman enhancement factor (EF), combining with confocal Raman microscopy systems. The result of scanning electron microscopy (SEM) shows that a large number of silver nanoparticles are attached onto the tips and sidewalls of the ordered carbon nanotubes array uniformly. EF of the sample which was produced 30 min annealing time and 450 ℃ annealing temperature evaluates to 2.2×103, and the reasons for the low EF are analyzed: on the one hand, thickness of silver film sputtered on vertically aligned carbon nanotube array is non-uniform, leading to distribution of silver nanoparticles is uneven after annealing, so that the value of sample roughness is too large, EF value is low; on the other hand, the excitation light source is not the advantage wavelength of silver nanoparticles in the experiments.