The Palace Museum houses a large number of exquisite artifacts with exotic styles. Among them, the black lacquer boxes inlaid with mother-of-pearl presented as tributes from Siam (Thailand) demonstrate the profound heritage of ancient cultural exchanges between China and foreign countries through their unique decorative techniques and production craftsmanship. This study employs scientific methods, including X-ray computed tomography (CT), pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), and high-throughput DNA sequencing to analyze the composition and structure of the substrates and lacquer layers of three such boxes. The results indicate that the lacquering material is thitsi, a kind of raw lacquer derived from the Melanorrhoea usitate tree cultivated in regions such as Thailand and Myanmar, which shows notable differences in texture and gloss compared with Chinese raw lacquer (urushi). The substrate exhibits a composite structure of “a wooden core as the base and rattan bundles for shaping”, with the core made of wood and rattan, consistent with the characteristics of local products in Southeast Asia. The lacquering process differs slightly from traditional Chinese lacquer manufacturing processes. This distinctive craftsmanship reflects both regional technical characteristics and the emphasis on the functions and aesthetics of foreign tribute artifacts of the period. This study enriches understanding of the diversity of the Palace Museum collection, provides important evidence for exploring material and cultural exchanges between East Asia and Southeast Asia during the Qing Dynasty, and offers a scientific basis and technical support for future conservation and restoration work.