Infrared spectroscopy, as an innovative exploration tool, enables rapid identification of alteration minerals, thus can facilitate an improved understanding of mineralization and enhance prospecting efficiency. This paper specifically applies this methodology to drill core samples from the Zhuxi Deposit, Jiangxi Province, the world's largest tungsten deposit. Using shortwave and thermal infrared spectroscopy, this study aims to identify spectral characteristics of typical altered minerals within the deposit, establish the mineral identification methods and preferred spectrum bands, and discern spectral characteristics of varied altered mineral combinations. The variations observed in the characteristic bands of these isomorphic minerals serve as indicators of changes in the ore-forming environment. Specifically, absorption features around 2190 nm are indicative of paragonite formation in low-temperature environments, while features around 2210–2225 nm signify the presence of phengite in high-pressure, high-temperature conditions. Absorption at 2260 nm is characteristic of Fe-rich chlorite, suggesting a low-temperature, reducing environment, whereas Mg-rich chlorite exhibits absorption at 2250 nm, indicative of a higher-temperature environment. Based on depth, the deposit can be classified into three types of alteration mineralization: greisen, garnet skarn, and diopside skarn. Shortwave infrared spectroscopy proves effective for identifying muscovite in greisen and altered minerals such as serpentine and chlorite in diopside skarn. Thermal infrared spectroscopy, on the other hand, is ideal for quartz identification in greisen and garnet in garnet skarn. Intriguingly, the study finds that the absorption characteristics of garnet can reflect the metal mineralization type of the deposit. The absorption valley wavelength of garnet varies from around 11290–11380 nm in non-mineralized or poorly mineralized samples, to 11230–11290 nm when scheelite mineralization dominates, and to 11180–11230 nm when both scheelite and chalcopyrite are present. These findings contribute significantly to our understanding of the mineralogical characteristics and genetic environment of the Zhuxi deposit. Moreover, they provide valuable insights into the potential application of infrared spectroscopy for skarn zonation and mineral exploration.