The overall layout of Xiange Tai (also known as Jueliang Ci) is symmetrical from the east to the west on the central axis, and the existing buildings are regulated as a three-entry courtyard, with the main gate, the halberd gate, Dacheng Hall, and Xiange Study Hall in turn from the south to the north. Dacheng Hall, as the most central building of Xiange Tai, boasting a magnificent appearance and beautiful colored drawings, has a width of seven rooms and a depth of five rooms, and is a single-eaved hiatus style building. Green glazed tiles covering the roof, corridors around and 24 square pillars of green stone supporting are the distinctive features of Dacheng Hall, which is unique among the Confucius Temples in China. Under the long-term influence of the natural environment and human factors, the painted surface of Dacheng Hall has suffered from a series of diseases such as color fading, cracking, pigment falling off, etc. The painting restoration work has become a prominent problem that needs to be solved for the current conservation of the cultural relics. We analyzed the layers and forms of the painted samples in detail, and conducted a comprehensive study from multiple angles, including the profile and surface, to find that 1) most of the painted samples consisted of the base layer, plaster layer and pigment layer in sequence from the inside out; 2) the plaster layer of the blue samples was made via the traditional single-layer plastering process; 3) the red samples had no plaster layer—the red pigment was painted directly on the base layer. It is speculated that this may have something to do with the development of the times and the changes in the craftsmanship. In order to better serve the scientific conservation of the cultural relics, it is necessary to understand the pigment composition and production process of color paintings of Dacheng Hall. In this study, modern technologies and methods such as super depth-of-field 3D microscopy, scanning electron microscopy-energy dispersive spectrometry and Raman spectrometry were used to analyze the layer structures, microscopic forms and compositions of the pigment samples. According to the profile observation results, the pigment layer of Dacheng Hall had more than two sub-layers, indicating that it had been repainted in history. Besides repainting, we also found the painting process of using one pigment (as the surface) covering another pigment (as the base). In terms of pigment materials, the red one was hematite, the blue ones were natural ultramarine and synthetic ultramarine and modern pigments were used for parts of the paintings. The plaster layer was mainly made via the calcite-based single-layer plastering process. In addition, it was also found that the thickness of the pigment layer of the painted samples varied from one another, and that falling off to different degrees appeared on some pigment surfaces. Therefore, the repair materials, cleaning and reinforcement methods used in the subsequent restoration need to be further studied. The results of the study provide key information for the identification of pigments and the selection of repair materials for Dacheng Hall and provide a scientific basis for the following conservation of painted cultural relics, avoiding problems such as “protective damages”.