The work aims to analyze color painting pigments of the World Cultural Heritage—Dagaoxuan Temple ancient architectural complex of the Imperial Palace, so as to provide a basis for withdrawing historical information of restoring color painting pigments, establishing files, judging the year of production and restoring the color paintings. Comprehensive analytical test was performed to the pigments samples of multilayer color painting in Dagaoxuan Temple by using polarized light microscopy (PLM), scanning electron microscope coupled with energy dispersive spectrometer (SEM-EDS), Raman spectroscopy (Raman) and other instruments. Sectional structure picture of multilayer pigments coated by resin was obtained. Particle morphology characteristics of 5 samples with a total of 12 layers of pigment were obtained by polarizing microscope and SEM. Elements and corresponding contents of all pigments were measured by SEM-EDS. Position information involving spectral peaks of the pigments was measured by Raman spectroscopy. The pigment composition of each layer in the multi-layer color painting samples was identified synthetically by a variety of means complementing and supporting each other. Green pigments mainly contain atacamite, malachite, olivenite and emerald green; blue pigments mainly contain azurite and ultramarine blue; red pigments mainly contain iron oxide red, cinnabar and minium; black pigment contains carbon black; and white pigment contains calcite. Traditional pigments are generally present in inner layer while modern pigments including synthetic ultramarine and Paris green are found in the outer layer.