Thirteen rock samples were collected for studying the variation of element content in the mineral during the alteration process from Xinjiang, China. The IED-6000 in situ micro energy dispersive X-ray fluorescence developed by CDUT was applied to get chemical and physical data from minerals. The non-destructive spectrometer is based on a low-power Mo-anode X-ray tube and a Si-PIN peltier cooled X-ray detector. The unique design of the tube’s probe allows very close coupling of polycapillary and makes the use of micro-area measurement feasible and efficient. The spectrometer can be integrated into any microscope for analysis. The long axis diameter of beam spot is about 110 μm. According to micro-EDXRF measurement, the tetrahedrite was corrected to pyrite, improving the efficiency and accuracy of the mineral identification. The feldspar of mineralized rock sample is rich in Cu and Zn which can be used as prospecting indicator elements. Element content of Cr, Mn and Co shows negative correlation with the degree of mineralization.