In order to make surface-enhanced Raman scattering (SERS) substrates contained more “hot spots” in a three-dimensional (3D) focal volume, and can be adsorbed more probe molecules and metal nanoparticles, to obtain stronger Raman spectral signal, a new structure based on vertically aligned carbon nanotubes (CNTs) coated by Ag nanoparticles for surface Raman enhancement is presented. The vertically aligned CNTs are synthesized by chemical vapor deposition (CVD). A silver film is first deposited on the vertically aligned CNTs by magnetron sputtering. The samples are then annealed at different temperature to cause the different size silver nanoparticles to coat on the surface and sidewalls of vertically aligned CNTs. The result of scanning electron microscopy(SEM) shows that Ag nanoparticles are attached onto the sidewalls and tips of the vertically aligned CNTs, as the annealing temperature is different , pitch size, morphology and space between the silver nanoparticles is vary. Rhodamine 6G is served as the probe analyte. Raman spectrum measurement indicates that: the higher the concentration of R6G, the stronger the Raman intensity, but R6G concentration increase with the enhanced Raman intensity varies nonlinearly; when annealing temperature is 450 ℃, the average size of silver nanoparticles is about 100 to 120 nm, while annealing temperature is 400 ℃, the average size is about 70 nm, and the Raman intensity of 450 ℃ is superior to the annealing temperature that of 400 ℃ and 350 ℃.