The Changkeng–Fuwan Au-Ag deposit is representative in South China, which is located in the southwest of the Qin–Hang metallogenic belt (QHMB). The Au and Ag orebodies are located in the same altered fracture zone, forming independent gold and silver orebodies respectively, with the characteristics of “upper gold and lower silver” in space. Three metallogenic stages have been identified: the pyrite–quartz–sericite stage, the polymetallic sulfide stage, and the quartz–calcite stage. The fluid inclusions (FIs) from the deposit are the two-phase liquid-rich (type I) and the pure liquid FIs (type II). The microthermometric measurements of type I FIs are characterized by temperatures of 158–282 °C and 146–289 °C and salinities of 0.35–9.88 wt.% NaCl equiv. and 0.18–11.70 wt.% NaCl equiv. The H, O, He, and Ar isotopic data show that the ore-forming fluids of the deposit were derived from a mixture of magmatic and meteoric fluids. The C and O isotopic data suggest that the carbon of the fluid may derive from a magmatic source. The S and Pb isotopic data indicate that the primary source of the metals in the Changkeng–Fuwan deposit may be a magma source. Based on the geological characteristics, FI microthermometry, and isotope data (C, H, O, He, Ar, S, and Pb), we propose that the Changkeng–Fuwan deposit should be classified as a far-source low-temperature magmatic–hydrothermal deposit.