The Forbidden City in Beijing is the world’s largest and most complete preserved ancient wooden structure buildings. 2016 has witnessed its fisrt restoration since its extablishment one handred years ago. The Yanxi Hall, which has a large area of colored paintings, is an exquisite hall in the rear of the Yangxin Hall and is one of the most important objects in this restoration project. The colored paintings have the function of decoration and conservation of the wood inside. The identification of the original materials in the colored paintings is important for the study of the craftsmanship and the judgement of the disease. As the concept of “restoration as the past” is one of the main theory for the conservation of the heritage in China, the original material study is important for the design of restoration. In this study, a set of integrated testing methods, including cross-section analysis method, back scattered electron (BSE) image, energy dispersive spectrometer(EDS), Raman spectroscopy(RS), fluorescence staining, enzyme-linked immune sorbent assay(ELISA), immunofluorescence microscopy(IFM) and pyrolysis gas chromatography mass chromatography (py-GC-MS), was put forward and utilized to demonstrate the pigments and binders of the colored paintings of the Yanxi Hall. The results showed that the pigments are ascribed to cinnabar, red ochre, ultramarine, malachite azurite and paratacamite. The plaster embossing was composed of quartz, talc, chalk or dolomite. Tung oil was the binder of the ground layer, while animal glue was used as binder in the pigment layer. When studying the colored paintings from the roof beams, a red pigment layer, which was composed of cinnabar, was found both at the bottom and inside of the ground layer. The red pigment layer was composed of two layers. The internal layer was made up of cinnabar and red ochre, which had the diameter of only about 1 μm, while the outer layer was composed of cinnabar, whose diameter distributed in the range of 1~30 μm. The red pigment layer inside the ground layer and the two red layer to decorate the suface are unique crafts for the colored paintings from the Yanxi Hall. These results demonstrate that this set of integrated methods has the advantages of micro destructive sampling and high reliability. It is an economical and practical method to investigate the pigments and binders of colored paintings.