In order to comprehensively understand the craftsmanship of a Guqin and also to provide a scientific basis for its restoration and conservation, we analyzed lacquer film and silk string fragments of a Guqin named “Yu Quan” made by Zhu Yuan, a famous expert of Guqin in the Yuan Dynasty. Utilizing various analytical methods, including stereomicroscopy, electron probe analysis, Fourier transform infrared spectrometry (FTIR), pyrolysis gas chromatography-mass spectrometry etc., we studied the micro-morphology, stratified structure, composition and lacquering technique of the Guqin. The results show that the body of the Guqin is made up of a wood body layer, a lacquer ash layer, a primer layer and a color lacquer layer. The application of the primer layer connects well the lacquer ash layer and the lacquer film layer. During the Guqin-making process, a lacquering technique utilizing a grey-painted lacquer was used to enhance the Guqin’s mechanical and waterproofing properties and also improve its playing effect. The main material of the lacquer ash layer is bone ash. FTIR showed that the strings were made from animal fibers. Furthermore, ESCAPE identification of organic matters showed that the lacquer film was composed of lacquer liquid, dry oil and starch. The lacquer liquid was probably derived from urushiol from lacquer trees (e.g., Rhus verniciflua, Rhus succedanea and Melanorrhoea sp.). The application of modern analytical instrumentation reveals hidden information contained in the Guqin to a certain extent. This research provides information on the preservation state, material composition, stratified structure and lacquering technique of the Guqin, and can be used to guide the scientific conservation and restoration of other unearthed lacquerware.