The Chayong Cu-polymetallic deposit is a recently discovered Cu-polymetallic deposit hosted in the Sanjiang Metallogenic Belt within the Tibetan Plateau of China to the northeast of the North Qiangtang terrane. The ore body occurs in siltstone and is controlled by a northwest-trending fault structure. According to the associations, assemblages, and cutting relationships between ore veins, the hydrothermal mineralization period can be divided into three mineralization stages: (1) a molybdenite mineralization stage, (2) a Cu-polymetallic sulfide stage, and (3) a quartz-carbonate stage. Two types of fluid inclusions (FIs), namely, liquid and vapor-rich inclusions, are present in quartz associated with sulfide minerals. Early-stage FIs are both liquid and vapor-rich, homogenized at temperatures ranging from 364.1 to 384.2 °C, and have salinities ranging from 0.70% to 9.60% NaCl equivalent (eqv). The middle-stage FIs are also both liquid- and vapor-rich, homogenized at temperatures ranging from 272.4 to 355.6 °C, and have salinities ranging from 0.53%–17.10% NaCl eqv. The late-stage FIs are liquid, homogenized at temperatures ranging from 209.4 to 255.3 °C, and have salinities ranging from 0.35%–6.87% NaCl eqv. The samples from the deposit have δ34S values of − 21.8‰ to − 19.2‰ and − 5.5‰ to − 6.0‰, suggesting that sulfur was derived from the host sediments and magmatic fluids, respectively. The metallic minerals within the deposit have 206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb values of 18.439–18.458, 15.656–15.679, and 38.772–38.863, respectively, suggesting that the metals were derived from the upper crust and orogenic belts. The samples from the deposit have δ18OW values of 2.99‰–7.99‰ and δDW values ranging from − 84.4‰ to − 73.9‰, indicating that the ore-forming fluids were magmatic and mixed with minor amounts of meteoric water. The ore-forming fluid of the Chayong copper polymetallic deposit was a high-temperature, medium- to low-salinity H2O–NaCl–CH4–N2 ± CO2 fluid system. The early high-temperature magmatic fluid, due to boiling, decreased in temperature, and via the mixing of meteoric water, gradually evolved towards the later-stage medium- to low-temperature and low-salinity fluid, causing molybdenite mineralization and forming copper polymetallic sulfide veins and quartz carbonate veins.