Nanshan Temple in Taizhou was once a royal temple but now is a historical and cultural site protected at the provincial level in Jiangsu. In 2019, Nanjing Museum designed a protection scheme for ancient architectural polychrome paintings in the Great Buddha’s Hall of Nanshan Temple. In this study, the paintings were tested and analyzed for the first time since the foundation of the People’s Republic of China. Small amounts of pigments were scraped as samples for a series of observations and analysis, including ultra-depth-of-field microscopy, X-ray diffraction (XRD), scanning electron microscopy-energy dispersive spectrometry (SEM-EDS) and Raman spectrometry. The results show that the red pigment is cinnabar, the blue one ultramarine blue, the green one lavendulan and the white one limestone. The detection and analysis results provide important information for the research on high-grade temple buildings in Jiangsu Province.