Abstract: The Yinachang Fe-Cu-REE deposit is one of the representative Proterozoic Fe-Cu-REE deposits in central Yunnan, at the southwestern margin of the Yangtze Block, China. Beside Fe and Cu, there are REEs, Nb, Mo, Co, Au, U and other elements in the ores. The study on the occurences of rare earth minerals and rare minerals is very weak. It is difficult to identify precisely using the traditional testing techniques and methods due to the relatively complex mineral composition, the small size and the complex dissemination characteristics of rare earth minerals and rare minerals in ores. In order to explore the occurrences of rare earth minerals and rare minerals, the Automated Mineral Identification and Characterization System (AMICS) was used. This system is the most up-to-date mineral automatic analysis system in mineralogy and geology in the world. Combined with the Scanning Electron Microscope and X-ray Energy Dispersive Spectrometer (SEM-EDS) microstructure in-situ analysis technique, this system was used to determine the species and contents of minerals in vein ores from the Yinachang Fe-Cu-REE deposit. The quantitative mineral identification, which was difficult to achieve by conventional means of rock-mineral identification, have been completed. The results show that there are 0.82% parasites and 0.02% Nb-bearing rutiles in the vein ores. Both of the iron oxides and copper sulfides mineralization stages are associated with REE mineralization in this deposit. Two main mineralization stages are identified, i.e., the Fe-REE mineralization stage (Ⅱ-1) and Cu (-Au)-REE mineralization stage (Ⅱ-2). This study provides accurate and reliable evidence for the comprehensive utilization of rare earth and rare metal resources and the further study of Fe-Cu-REE deposits. An advanced and practical technical method of rock-mineral identification was established, which is expected to be more widely used in fields such as geology, exploration and effective utilization of mineral resources.