Many ancient Asian and Japanese paintings have been drawn with natural mineral pigments. The discoloring mechanism of these pigments has been a real concern for the characterization, restoration and preservation of the ancient cultural properties. The authors expect that the color fading is deeply related to the chemical composition and the fine structural change of the major elements. Therefore the purpose of this paper is to make clear the relation between the fine structural change and color fading. We analyzed several representative pigments from Japan, including copper carbonate hydroxide pigments (azurite and malachite, “gunjo” and “ryokusho” called in Japanese) by x-ray fluorescence analysis (XRF) and x-ray absorption fine structure (XAFS). In order to examine the deterioration of pigments, some of them were exposed to a heated condition of 260[degree]C under oxidizing condition, as is a common practice in the preparation of pigments in Japan. The spectral reflectivity was collected on spectrophotometer system at 10 minutes intervals. Here we propose to compare the results obtained from XRF and XAFS with the spectral reflectivity. The results demonstrate that the chemical composition and the fine structural changes can provide valuable information for revealing the discoloring mechanism, and this then leads to an original color deduction of the ancient cultural property.