The Middle–Lower Yangtze River Metallogenic Belt (MLYRB) is one of the most important Cu–Au–Fe–Mo skarn–porphyry metallogenic belts in Eastern China. After several decades of mining, the shallow-level mineral resources have been gradually exhausted, which call for new exploration tools for concealed orebodies. The Tonglushan Cu–Au–Fe skarn deposit (86.3 Mt @ 1.66% Cu, 0.94 g/t Au and 39.4% Fe) is located in the western MLYRB. Skarn alteration/mineralization are mainly hosted in the contact zone between Cretaceous (~141 Ma) quartz monzodiorite (and its porphyry) and the Lower Triassic carbonate rocks. Based on the mineral assemblages and their macro/microscopic textural relationships, the Tonglushan Cu–Au–Fe mineralization/alteration can be divided into five stages: pre-ore (S1: skarn–potassic alteration), Fe ore (S2: retrograde alteration and Fe-oxides), Cu–Au ore (S3: quartz–sulfides), carbonate alteration (S4) and supergene alteration (S5). Apart from the major skarn and retrograde alteration and carbonate minerals, abundant fine-grained phyllosilicate minerals, including chlorite, white mica (illite, muscovite and phengite), smectite (montmorillonite and saponite) and kandite (kaolinite, dickite and halloysite) group minerals have been identified at Tonglushan by SWIR spectrometry. Integrating petrographic observations and SWIR spectral analysis, four alteration zones (with distinct phyllosilicate assemblages) have been distinguished from the intrusion outward: (I) ore-barren quartz monzodiorite and its porphyry (montmorillonite–illite–chlorite), (II) endoskarn close to the skarn–hydrothermal mineralization center (montmorillonite–illite–chlorite–kaolinite–dickite), (III) skarn–hydrothermal mineralization center (saponite–chlorite), and (IV) the external contact zone in (dolomitic) marble (montmorillonite–chlorite ± kaolinite ± dickite).For the Tonglushan altered rock samples, SWIR spectrometry has identified wavelength shifts in the Fe–OH, Al–OH and sub-Al–OH absorption features of chlorite, white mica–montmorillonite and kandite, respectively. Chlorite Fe–OH absorption occurs at longer wavelengths (>2,250 nm), white mica–montmorillonite Al–OH absorption occurs at unusually long (>2,212 nm) and short (<2,202 nm) wavelengths, and kandite sub-Al–OH absorption occurs at longer wavelengths (>2,170 nm) in strongly-altered skarn proximal samples. Moreover, the presence of kaolinite, dickite, saponite, actinolite, phlogopite and/or chlorite–quartz–sulfides veins in these samples can be used as new vectors to explore deep-level mineralization centers at Tonglushan. The distribution of various kinds of phyllosilicate alteration minerals at Tonglushan, especially the white mica and kandites (with higher crystallinity) in the deep contact zones, indicates that the neutral to acidic hydrothermal fluids may have been generated with the precipitation of Fe-oxides and sulfides. This study also highlights the potential of SWIR spectroscopy of phyllosilicate minerals for exploring concealed skarn orebodies in the MLYRB.