The aim of this study was to analysize the blue and green pigment samples falling off from the Thangka Portrait of Vajrabhairava. 3D video microscope was applied to observe the morphology, particle size distribution, impurity. Laser Raman spectrum, infrared absorption spectrum, X-ray diffraction spectrum were used to show the chemical composition and crystal structure. According to the mutual confirmation of various spectral analysis results, the main component of blue pigment was azurite, while the main component of green pigment was malachite with good crystal structure. The spectroscopic method can provide a reference basis for the selection and protection of materials with a view the protection, repair and preventive protection of Thangka.