The Mississippi Valley–type (MVT) deposits reached their maximum abundance during the final assembly of Pangea. The intense orogenic activity during this assembly in relatively low latitudes created abundant opportunities for the migration of sedimentary brines into the interior carbonate platforms landward of the orogenic belts, leading to the formation of MVT deposits. Thus, dating the MVT deposits can potentially aid in the reconstruction of the plate tectonic evolution during the assembly of Pangea. The Yangtze Craton hosts significant carbonate-hosted Zn–Pb deposits (> 60 Mt Pb + Zn metals), accounting for 30% of China’s Zn–Pb resources. However, determining the timing of zinc and lead mineralization in these reservoirs is challenging. This study employs LA-ICP-MS U–Pb geochronology on calcites to date Zn–Pb deposits hosted in Lower Cambrian limestone in the Huayuan orefield. Three generations of calcite formation were dated: the first recorded the pre-ore deposition of Lower Cambrian limestone at 517 ± 10 Ma, the second marked a hydrothermal event linked to stratiform sphalerite ore formation at 501.4 ± 8.4 Ma, and the third was associated with discordant breccia-hosted Zn–Pb mineralization at 397.5 ± 9.6 Ma. Our results indicate that Paleozoic carbonate-hosted Pb–Zn mineralization in the Yangtze Craton is linked to (1) the final assembly of Gondwana in the late Cambrian-early Ordovician (520–480 Ma); and (2) the intracontinental orogeny response to Jiangnan Uplift (420–400 Ma). This study highlights the temporal relationship between low temperature carbonate-hosted mineralization and orogenic events that are consistent with classic MVT models worldwide. It also contributes geochronological data for the reconstruction of plate-tectonic evolution during Pangea assembly. Furthermore, it demonstrates the potential of in situ U–Pb calcite geochronology to date ore deposits lacking syn-ore minerals suitable for traditional dating methods.