The effects of the pulsed green laser annealing at ambient nitrogen for two different heights-CNWs grown on silicon substrate were investigated on the crystallinity and morphology using Raman spectroscopy, SEM, TEM and XPS. For the 1μm height-CNWs, the peak intensity of D-band spectra decreased as the laser energy density increased up to 1.3Jcm-2, ID/IG ratio decreased from 2.5 to 0.7. The crystallinity of CNWs was improved by the laser irradiation. For the 1μm height-CNWs irradiated above 1.5Jcm-2, the height of CNWs decreased gradually as the laser energy density increased, it was clarified that the surfaces of CNWs were vaporized by the laser irradiation. For the 20μm height-CNWs, the peak intensity of D band spectra also decreased until the laser energy density increased up to 0.8Jcm-2, ID/IG ratio decreased from 1.6 to 0.5. From the TEM observation of CNWs irradiated at 0.8 Jcm-2, it was confirmed that the laser irradiation changed CNWs to be highly oriented crystal structure. However above 0.8Jcm-2, the crystallinity was deteriorated due to the vaporization of CNWs as the same as the 1μm height-CNWs. The pulsed green laser annealing is effective to improve the crystallinity of CNWs on optimal laser energy density for both height-CNWs, the higher laser energy densities vaporized the CNWs and changed the morphology and crystallinity of CNWs.