The complexity of geological processes created the macroscopic and microcosmic characteristics of geological samples with inhomogenous features. These features can be revealed effective through spectroscopy analysis technology. This study took the ore and surrounding rock samples from Jinshan Ag-Au deposit of southern Qinzhou-Hangzhou metallogenic belt while carrying out macroscopic geochemical characteristic and microcosmic characteristics analysis based on the X-ray fluorescence spectroscopy, plasma mass spectrometry and Raman spectrum. The results showed that the main elements of ore and surrounding rock had great differences while the distribution patterns of trace element and rare earth element were similar. It reflected that the trace elements and rare earth elements showed high geochemical stability in the process of mineralization. Raman spectral characteristics of quarts showed that the peak at 507 cm-1 did exist in ore samples, but disappeared in surrounding rock samples. It indicated that the ore and surrounding rock went through different temperature and pressure in the ore-forming process, and the peak could be used as the signs of whether exists mineralization. Comparison with the Raman shift next to 463 cm-1 for quartz between ore and surrounding rocks, the FWHM and integral strength of fitting peak denote that the quartz in ore samples have better crystal degree than that of quartz in country rocks . These quartz microstructure changes should be subjected to the late hydrothermal activity. The quartz in the surrounding rock is influenced by the late hydrothermal, part of the ore-forming fluid may be from surrounding rock, and the ore-forming fluid has multiple phase, the crystallization degree of mineral was in different stages, causing different FWHM.