The Yangshikeng mercury deposit in southeastern Chongqing is a carbonate-hosted Hg deposit within the South China low-temperature metallogenic domain, but its metallogenic age and genetic mechanism remain unclear. In this study, we present integrated in situ U-Pb dating of calcite from the main mineralization stage, together with trace element and C-O-Sr isotopic analyses of calcite from different mineralization stages to constrain the ore-forming process. Calcite U-Pb dating yields two age populations: a main mineralization age of 217 ± 12 Ma and a younger age of 114 ± 56 Ma. The Triassic event corresponds to the collision between the Indochina Block and the South China Craton, which induced intense regional compression and generated large-scale fault systems that facilitated deep fluid circulation and basinal brine formation. The Cretaceous age may record later hydrothermal disturbance or overprinting. Calcites from the main mineralization stage (Cal-I) have elevated ⁸⁷Sr/⁸⁶Sr ratios (0.7135–0.7187), which are higher than those of marine carbonates (0.7080–0.7110) and comparable to the Neoproterozoic Banxi Group basement (0.7131–0.7281), indicating contribution from the basement source. Late-stage calcites (Cal-II) show a wider range of ⁸⁷Sr/⁸⁶Sr ratios (0.7091–0.7198), overlapping the host dolostone. They display increased total REE contents and weakened LREE/HREE fractionation, indicating a contribution from the host rock. These integrated geochemical constraints suggest that the ore-forming materials of the main mineralization stage are derived from a radiogenic basement source, whereas the late stage involved mixed contributions from the Qingxudong Formation wall rock and early-stage calcites through recrystallization or fluid–rock interaction. The main mineralization stage is related to a relatively closed basinal brine system, while the late stage records fluid mixing and progressive opening of the system.