This study analyzes the pigments and binders used in the painted wooden structure of DaZhong Gate in the Confucius Temple in Qufu, Shandong Province, China. Five samples were collected from the building and analyzed using techniques such as polarized light microscopy (PLM), energy-dispersive X-ray spectroscopy (EDX), micro-Raman spectroscopy (m-RS), and Fourier-transform infrared spectroscopy (FT-IR). The findings reveal that the red, yellow, green, and blue pigments are identified as lead red, lead chromate yellow, emerald green, and ultramarine, respectively. The white pigment is determined to be a combination of chalk and lead white or anglesite. Considering the production period of the yellow and green pigments, it is inferred that architectural paintings underwent restoration or repainting during the late Qing Dynasty. The analysis of the binder in the pigment using pyrolysis–gas chromatography/mass spectrometry (Py-GC/MS) reveals that the binder employed is a protein-based glue. Additionally, the detected presence of Heat-bodied tung oil suggests a potential connection to traditional Chinese painting techniques on wooden surfaces. This discovery not only contributes to the historical research of the Confucius Temple but also provides crucial data for the conservation and restoration efforts of this culturally significant heritage site.