Compositional variations of chlorite have been increasingly used to trace the magmatic–hydrothermal fluid evolution, as well as exploration vector toward concealed orebodies. This method has been widely applied to porphyry Cu (–Au) systems, but related research on skarn systems remain scarce. The Tonglushan Cu–Au–Fe deposit (86.3 Mt @ 1.66% Cu, 0.94 g/t Au and 39.4% Fe) is one of the largest Cu–Au polymetallic skarn deposits in the Middle–Lower Yangtze River metallogenic belt (MLYRB, Eastern China). Based on detailed petrographic observation, we present new EPMA and LA–ICP–MS elemental data for the Tonglushan chlorite, and discuss their implications on hydrothermal fluid evolution and exploration of concealed skarn orebodies there. At Tonglushan, chlorite alteration is well developed in the main Cu–Au sulfide ore stage. Three types of chlorite have been identified, i.e., disseminated chlorite replacing biotite and/or hornblende in the ore-causative quartz monzodiorite (porphyry), vein-type chlorite in quartz–chlorite–sulfides veins along/near the internal and external intrusive contact, and replacement-type chlorite that replaced garnet, diopside, epidote and Fe oxides in the skarn mineralization center.All the Tonglushan chlorite samples belong to trioctahedral chlorite and have similar crystallization temperatures (163–351 °C). The substitution mechanisms of Fe2+ ⇔ Mg2+, Tschermark (AlivAlvi ⇔ Si (Mg2+, Fe2+)) and di-trioctahedral (3(Mg2+, Fe2+) ⇔ □ + 2Alvi) are likely important for the Tonglushan chlorite formation. Replacement-type chlorite shows higher contents of FeOT, mobile elements (e.g., Ca, Na, B, Sr, Pb, Zn and Sn) and ore-forming elements (e.g., Cu and Co), whereas the disseminated chlorite has higher contents of Ti, Li, LILEs (e.g., K, Rb, Ba and Cs) and incompatible elements (e.g., V, Sc, Co and Ni). Meanwhile, the vein-type chlorite has similarly high contents of Ti, Li, V, Sc and Ni to the disseminated chlorite, but has higher FeOT and Cu contents but lower MgO content than the latter. Such compositional differences may have mainly attributed to the protolith (or precursor minerals) and hydrothermal fluid chemistry. Integrating the chlorite petrographic features and chemical compositions, we suggest that elevated FeOT and B contents and Fe/(Fe + Mg) ratios, and lower MgO, Al2O3, Ti, V and Sc contents can serve as proximal indicator for exploring concealed skarn orebodies at Tonglushan, as well as other similar Cu–Au–Fe skarn deposits in the MLYRB.