The Jiama porphyry- skarn type copper polymetallic deposit is an important super- large porphyry- skarn- hornstone type deposit in theGangdise metallogenic belt. As the first solid mineral research drill in the Qinghai- Tibet plateau, the 3000 m deep drill penetrated the hornstone, skarn and porphyry ore bodies into the deep barren core, which is of great significance to reveal the metallogenic system of the Jiama porphyry. In this paper, short wave and thermal infrared technique were applied to test and analyze the spectrum of the 3000 m deep drill of the Jiama mine, the spatial distribution and content variation of the main minerals in different metallogenic systems are identified, and the significance of exploration indication of important altered minerals is also revealed. The results show that biotite, albite, orthoclase, quartz, muscovite and chlorite are mainly recognized in the hornstone, and the feldspar is mainly albite and orthoclase, while the chlorite is mainly Mg rich chlorite and Fe rich chlorite. The skarn minerals such as garnet, diopside, wollastonite and vesuvianite are recognized in skarn, and the garnet is mainly andradite. Feldspar, quartz, mica, hornblende and chlorite are recognized in porphyry and porphyrite, among which chlorite is mainly Fe rich chlorite and mica is mainly muscovite. Among them, longwave chlorite and longwave muscovite can indicate the mineralizing center and hydrothermal center of porphyry- skarn- hornstone, and longwave garnet can effectively indicate the proximal position of skarn. The main minerals can be distinguished by the FMI of thermal infrared. The whole skarn is between 9470 nm and 11600 nm, the FMI values of garnet and diopside are the largest, the content of FMI is the highest, and the whole hornstone is between 8500 nm and 9000 nm. The FMI values of mica and chlorite are lower than those of skarn, and the whole FMI changes little in porphyry, which lies between 8500 nm and 9280 nm. In hornstone and porphyry, the Pos2200 of mica less than 2206 nm corresponds to the better Cu- Mo mineralization, and the Pos2200 of mica short- wave movement in the hornstone corresponds to the strong Cu- Mo mineralization, and the Pos2200 of mica in skarn is between 2209~2212 nm; Pos2250 of chlorite in skarn and porphyry indicates the occurrence of strong Cu- Mo mineralization, while the position of “T” absorption peak of garnet is more than 11500 nm, which generally corresponds to strong Cu mineralization. The research results of this paper prove that the shortwave- thermal infrared technique can provide effective technical support for deep exploration and prospecting of the Jiama porphyry- skarn- hornstone metallogenic system.