H2O2/ultraviolet (UV) radiation treatment was proposed to simulate burial-induced degradation of natural dyes. The method was applied to the major pigments of Phellodendron bark, madder, and indigo plant, and their silk dyeings, and the degraded samples were analyzed using high-performance liquid chromatography-diode array detector-mass selective detector (HPLC-DAD-MS). Retention times of the HPLC chromatogram, UV-visible λmax obtained from DAD analysis, and major ion detected by the MS analysis were used to identify berberine, palmatine, alizarin, purpurin, indigotin, and indirubin included in dye solution and the extraction from silk dyeing. Alizarin, purpurin, and indirubin were more susceptible to degradation by H2O2/UV than berberine and palmatine. Indigotin was completely degraded with 5 minutes of treatment, producing isatin as the degradation product. Alizarin, purpurin, and indigotin were more resistant to degradation when they were affixed to the fibers.