The Yushui ore deposit, located in the middle section of the Yong’an-Meixian Hercynian depression, is a medium-sized Cu-polymetallic massive sulphide deposit in Eastern Guangdong Province, South China. This deposit is characterized by unusually high copper grade (up to 50–60 wt. % Cu). Other metallic elements, such as lead, zinc and silver, are also economically important in the Yushui ore bodies. The aim of this study was to apply N2–Ar–He systematics, together with organic gases (light-hydrocarbon tracers), to constrain the origin and evolution of ore-forming fluids. The helium-argon isotopes and trace gas compositions of fluid inclusions trapped within metal sulphide minerals were measured for a number of bonanza ores from the Yushui deposit. The noble gas concentrations in the studied samples vary over one to two orders of magnitude (4He: 2.27–160.00 × 10−5 cm3 STP g−1; 3He: 0.53–34.88 × 10−12 cm3 STP g−1; 40Ar: 6.28–37.82 × 10−7 cm3 STP g−1; 36Ar: 1.25–10.40 × 10−9 cm3 STP g−1). Our data show a narrow range of 3He/4He ratios from 0.006 to 0.056 Ra (~0.026 Ra on average, n = 8), which are considerably lower than the modern atmospheric end-member value; whereas the 40Ar/36Ar ratios (ranging from 333.76 to 501.68, with an average of 397.53) are significantly greater than that of air-saturated water. Most of the bornite samples have somewhat higher 3He/4He ratios of trapped fluids when compared to chalcopyrite. Overall, these He-Ar results are well within the range of crustal reservoir, thus implying a predominantly crustal source (originated from Caledonian basement) for ore-forming solutions, with little contribution from mantle-derived fluids. Analysis of the N2–Ar–He composition in Cu-rich sulphides indicates that the Yushui ore-forming fluids were probably derived from formation water (or basinal hot brines). Moreover, organic gas species identified in sulphide-hosted fluid inclusions are mainly composed of C1–C4 alkanes, while the concentrations of unsaturated olefins and aromatic hydrocarbons are very low. In particular, most chalcopyrite samples with relatively low 3He/4He ratios (0.006–0.016 Ra) and 40Ar*/4He values (0.0002–0.0012) are generally characterized by very high CO2/CH4 ratios (~60–102). All these suggest that main-stage Cu-Ag metallogenic processes might have not been affected by high-temperature magmatic activities or superimposed by strong metamorphic overprinting, although some chalcopyrite-rich ores appear to be influenced by later stage hydrothermal processes. In summary, neither magmatic input nor convecting seawater has played an important role in the formation of Yushui copper-polymetallic deposit. The massive sulphide ore bodies were products of water–rock interaction between metal-bearing basinal brines and the host sedimentary strata.