The Jiulong calcite deposit, located in the southwest margin of the Yangtze Platform, is a large scale giant crystal calcite deposit, which is the largest calcite ore deposit with economic orebodies in centralized outputs so far in northwestern part of Central Yunnan Paleozoic Basin, central Yunnan Province, SW China. The proved orebodies are mainly hosted along the beddings of the hosting limestones in the stratiform and stratiform-like shape, and some exist in the interlaminarg and steeply dipping fault zones in the form of large vein types.And the middle successions of the Lower Permian Maokou Formation (P1m) limestone is the main ore-hosting rocks. Up to now, the ore genesis is still unclear. In this paper, based on geological investigation and petrographic observation, the giant crystal calcite ore zone, dolomitizated hosted rocks zone, and mottled calcite hosted rocks zone are selected to carry out mineral chemistry, C–O isotopic composition and fluid inclusion analysis of different types calcites and ore-hosted rocks, and calcite U–Pb dating. The results show that the Jiulong calcite deposit is a low-temperature hydrothermal deposit with outstanding characteristics of epigenetic origin, replacement and filling of hydrothermal fluid ? and structure- controls. The ore-forming fluid is featured by Cl–Na·Ca type basinal brine in nature, which mainly comes from the cyclic reaction of ore-hosting rocks and underlying basement sediments. And there possiblely may occurr deep magmatic hydrothermal contributionAnd the oxidation of ore-forming fluid and the water-rock interaction gradually weaken from the surrounding rock to the orebody through the transition zone. Tiny variation of the temperature gradients , slow nucleation rateand long time crystallization? process are the key mineralizing mechanisms of this large-scale giant crystal calcite deposit. The metallogenic timing is the Eocene–Oligocene, and is a tectonic result f the Cenozoic Indo–Eurasian collision orogeny in the Central Yunnan Paleozoic Basin.