Caisson paintings are an integral part of the unique interior decoration ceiling of traditional Chinese architecture. There are a large number of Yuan Dynasty caisson paintings in the Puzhao Temple, in Hancheng, Shaanxi Province, China. These caisson paintings have exquisite patterns and rich colors, which are rare artistic treasures of the Yuan Dynasty. In the history of nearly 700 years, due to various environmental and human factors, the caisson paintings have experienced various degradation; for example, the paper of the caisson paintings is acidified, the surface is polluted, the color is faded, mottled, and it is difficult to identify. Therefore, their protection is vital. In order to ensure the scientific and targeted development of the protection scheme, this study conducted a comprehensive and in-depth analysis of the paper fibers, pigments, adhesives, wood supports, and pollutants of the caisson paintings and carried out a series of protection experiments in the field and laboratory, providing a step-by-step review of the protection treatment application for the caisson paintings. Mechanical and wet cleaning were used to remove the pollutants. The caisson painting was deacidified with a barium hydroxide ethanol solution, and the paper and pigments of the caisson painting were strengthened with water-based fluorine. Several conservation problems, such as the removal of pollutants, the deacidification of acidified paper, and the reinforcement of flaking paper and pigments, were solved. Meanwhile, good conservation and restoration results for caisson paintings were obtained. This research method of combining theory and practice has greatly improved the scientificity and success rate of conservation work. These research results provide valuable experience and reference for other caisson paintings in similar environments.