The stone relics in the Meili section of the ancient Tea Horse Road in Yunnan, China, are important for Sino-Tibetan cultural heritage. However, these relics were exposed to the risk of hydraulic erosion due to the construction of a hydroelectric power station, and thus protecting these relics is now imperative. Preliminary investigations and analyses of stone relics are crucial for their subsequent conservation and restoration. Thus, in this study, multi-analytical characterization including the microstructure, mineralogical characteristics, elements, and chemical compositions of the stone relics was conducted using optical microscopy (OM), scanning electron microscopy-energy dispersive spectrometry (SEM-EDS), polarized light microscopy, x-ray diffraction (XRD), and attenuated total reflection-Fourier transform-infrared spectroscopy (ATR-FTIR). In addition, the contaminants and pigments on the surfaces of the stone relics were identified and analyzed by Raman spectroscopy. OM, SEM and Raman spectroscopy indicated that the surface contaminants mainly comprised of moss and soil dust, and some of the stone relics exhibited porosity and weathering. Polarized light microscopy revealed that the mineralogical morphology of stone samples mainly appeared as allotriomorphic, hypidiomorphic, and colloform structures. ATR-FTIR, and XRD confirmed that the stone relics mainly consisted of quartz, muscovite, illite, and chlorite. In addition, Raman spectroscopic analysis showed that the pigments on the relic surfaces included chalk, barium white, langite, green earth, amorphous carbon black, chrome red, and chrome yellow. The findings of this study may provide scientific support for the conservation of the stone relics.