Carlin-type gold deposits are among the most important gold-bearing hydrothermal ore systems and are mainly located in Nevada, USA, and southwestern China. However, the source and evolution of the ore-forming fluids for these deposits remain controversial, especially those found within China. In this study, lithium and oxygen isotopic analyses of quartz-hosted fluid inclusions are used to elucidate the source and evolution of the giant Shuiyindong Carlin-type gold deposit. Fluid inclusions trapped in quartz of three distinct genetic stages have low salinity (0.8–6.3wt% NaCl equiv.) and moderate temperature (154–343 °C), but display variable Li and O isotope signatures. The Li and O isotopes of stage I fluids (δ⁷Li values from + 5.1 to + 9.1‰; δ¹⁸O values from + 6.3 to + 10.0‰) indicate predominantly a magmatic source for the initial ore-forming fluids. The large variations of Li and O isotopes of stage II fluids (δ⁷Li values from + 9.3 to + 16.0‰; δ¹⁸O values from + 0.1 to + 7.7‰) suggest that the fluids are controlled by mixing of magmatic fluids and meteoric water, which in turn triggered the precipitation of gold-bearing sulfides. The isotopic compositions of stage III fluids (δ⁷Li values from + 15.5 to + 22.8‰; δ¹⁸O values from − 5.4 to − 2.8‰) confirm that the final fluids are dominated by meteoric water. Furthermore, this work demonstrates that the combined Li–O isotopic analysis of fluid inclusions is a powerful tracer to decode the source and evolution of ore-forming fluids in hydrothermal mineralizing systems.