Abstract: Since isomorphous properties are common in many natural minerals, it is difficult to distinguish these minerals due to their similar characteristics under a microscope. The chemical composition and structure of these kinds of minerals can be obtained by using X-ray Diffraction Analysis, Electron Microscope Analysis, Electron Microprobe Analysis and Ion Probe Analysis, which can provide useful information for mineral identification. Galena (Pb 86.60%, S 13.40%) and sphalerite (Zn 67.10%, S 32.90%) contained in lead-zinc ore are more typical and are readily available to use as examples. The characteristic of minerals were determined preliminarily under the optical microscopy, and then the lead-zinc ore were qualitatively determined by using the in-situ micro-analysis function of RIGAKU ZSX Primus X-ray Fluorescence Spectrometer, which was applied to explain various characteristic of minerals. The experimental results show that the anomaly elements (S, Pb, Zn and Cd) were distinguished in some lead-zinc ores. According to the distribution analysis of the anomaly elements (Zn, S, Fe and Cd) in some sphalerite, 2D or 3D distribution images were established and the anomaly areas of elements are highly consistent. Under the real-time monitoring by charge-coupled device, the target area at the ore sample was quantitatively analyzed to identify the ore with its theoretical chemical components. The relative standard deviation (RSD, n=11) of determination of sphalerite sample components was less than 4%, which is comparable to the values obtained by Electron Microprobe. A new in-situ micro-analysis method of determining major and minor elements in lead-zinc ore is presented and is proved to be a fast non-invasive analytical technique. On the basis of the above analysis, a novel reasonable qualitative or quantitative analytical method for the identification of lead-zinc ore has been established, which provides a new method for the identification rock and minerals.