In order to analyze the effect on surface enhanced Raman scattering (SERS) properties of threedimensional (3D) substrate during evaporation process of the probe molecules solution, a 3D composite structure of silver nanoparticles modified vertically aligned carbon nanotubes array(Ag/CNTs) is produced by magnetron sputtering and thermal annealing processes. Relevant experiments use the time-course SERS mapping test method and select 1 μmol/L Rhodamine 6G (R6G) and 10^-2 μmol/L malachite green (MG) as probe molecules respectively. The results indicate that: with the increase of evaporation time, the Raman signal of probe molecules enhance firstly and then decrease. It is this main reason that, during evaporation process of analyst molecule, the capillary forces make the hotspots between the probe molecule and three- dimensional structure change, and then lead the electromagnetic field enhancements to change; in addition, the depth of focus and concentration change also influence the Raman signal.