This paper briefly describes the functions and characteristics of the SEM-EBSD-EDS-CL system(FEI Quanta 650 FEG SEM). Based on the system, the authors studied mineral and elemental characteristics of garnet, dolomite and nephrite. This system has many significant advantages, such as multi-work mode, easiness of sample preparation, high quality spectra, digital information processing and application of technological integration. The SEM-EBSD-EDS-CL system has a good vista in its application to the study of gems.