The statue of Yuanjue Cave in Anyue Grottoes was built in the Tang Dynasty, flourished in the Five Dynasties and Song Dynasty, which has the characteristics of inheriting Longmen and Yungang Grottoes and inspiring Dazu Rock Carving. It occupies an important position in the history of Chinese Buddhist grotto art. Due to the humid semi-open-air natural environment, improper restoration, and other human factors, a large area of pigment chalking, peeling, and flaking appeared on the statue's surface, and some were covered with modern pigments. However, there is a lack of relevant scientific analysis. To realize the conservation and restoration of the painted statues, it is necessary to analyze the composition and process of the original painted pigments. In the research process, we mainly use the combination of microscopic analysis, scanning electron microscope-energy spectrum analysis, and micro-area Raman spectroscopy to comprehensively determine the pigment composition and hierarchical structure and summarize the painting process of AnyueYuanjue Cave. At the same time, we will discover the phenomenon of pigment repainting and initially explore the relationship between pigment repainting and pigment flaking disease. The experimental results show that the color painting of Yuanjue Cave is based on a white power layer, and gypsum or calcite is used as the base material. This is consistent with the period of cave excavation and restoration. The surface decoration materials use a variety of traditional pigments: red pigments are hematite and vermilion, orange pigments are minium, green pigments are malachite, blue pigments are ultramarine, black pigments are carbon, and gold is gold. In addition, combined with the microscopic section and Raman results, a variety of modern synthetic pigments are also found in K7, K9, and K42, such as lead-chrome yellow, Prussian blue, and lavendulan (the decomposition of emerald green), etc., indicating that the statue was later painted. Multiple repainting increases the overall thickness of the pigment layer, and differences in the properties of the pigment binding medium may exacerbate the production of pigment flaking disease. This study provides a scientific basis for identifying colored pigment and the protection and restoration of Yuanjue Cave.