The Chating Cu-Au deposit in Xuancheng City, Anhui Province, is characterized by porphyry-style mineralization with intensive hydrothermal alteration. Short-wave infrared reflectance spectroscopy was used to systematically analyze the alteration of drill cores from two cross sections. Eleven alteration minerals—sericite, smectite, kaolinite, dickite, chlorite, epidote, gypsum, carbonate, iron oxide, saponite, and prehnite—were identified, and the relative abundances of individual minerals at various depths were calculated by depth of absorption peak. In these minerals, iron oxides and gypsum are probably related to supergene process and other alteration minerals are hydrothermal alteration minerals. The mineral assemblages and their spatial distributions indicate that the alteration patterns in this Cu-Au deposit were controlled mainly by water–rock interaction of the magmatic–hydrothermal process, resulting in a typical porphyry-style hydrothermal mineralization system. A saponite–smectite–K-feldspar–anhydrite (gypsum) alteration assemblage is located mainly in the host quartz diorite porphyry, and is minor in the wall rocks of limestone and a post-mineralization diorite porphyry. A sericite–chlorite alteration assemblage was widely developed in the quartz diorite porphyry, and the intensity of alteration decreases gradually outward from the center to the margins of the deposit. A kaolinite–calcite alteration assemblage is mainly located on the top of the quartz diorite porphyry and in the surrounding limestone. The physiochemical conditions of the hydrothermal fluid, such as temperature and pH, control the compositional variations of specific alteration minerals. The most remarkable feature is a subtle change in octahedral Al cation content of sericite, as identified by the change in wavelength of sericite Al-OH absorption peak position. Muscovite is the main component of sericite, with a trace amount of phengite. The Cu-Au grades are negatively correlated with the wavelength of sericite Al-OH absorption peak position, because high ore grades are associated with relatively shorter Al-OH wavelengths, corresponding to a high Al/Si ratio in sericite (i.e. towards muscovite). This correlation suggests that the ore metal tends to be enriched and precipitated in an acidic environment of the alteration system. In addition, a lateral variation across the deposit in Al-OH wavelength indicates that the acidity of the hydrothermal fluids decreases gradually from the center of the deposit outward to the wall rocks, whereas the variation of sericite Al-OH wavelength with depth suggests an increase in fluid pH with decreasing depth. The alteration patterns imply that during mineralization the ore-forming fluids probably migrated from the southwest in the deep part of the porphyry system towards the northeast near the surface. Based on the spectral alteration mapping, it is concluded that there were at least three stages of hydrothermal activity in the Chating mining district: an early potassic–skarn hydrothermal alteration stage, an intermediate propylitic–sericite medium-low temperature alteration stage, and a late kaolinite–dickite epithermal stage. The sericite alteration stage is temporally related to Cu-Au mineralization, leading to the formation of the main orebody at Chating. As the current exploration is still focused in the sericite alteration zone, it is inferred that deep exploration has great potential in the Chating district.