The Kunyang phosphate deposit, located on the southwestern margin of the Yangtze Block in southern China, is hosted by the Lower Cambrian Meishucun Formation. The distribution of the deposit is restricted, and the outcrops of its phosphate layer are intermittent, probably owing to subsequent regional uplift and erosion. Therefore, investigating the denudation and uplift history of the deposit can clarify the preservation and distribution of the ore body after its formation, providing insights into the geological evolution of the mining area. Petrographic analysis indicates that collophane is the main ore mineral in the phosphorite, accompanied by dolomite, quartz, and limonite. The bulk-rock geochemical analyses suggest that the formation of phosphorite took place in a marine environment characterized by relative oxidation and high salinity, possibly involving hydrothermal activity during a drier mineralization stage. Apatite fission-track thermochronology, zircon-apatite (U-Th)/He dating, and thermal history modeling demonstrate that the Kunyang phosphate deposit underwent rapid uplift process during the Late Triassic (c. 225–211 Ma) and Eocene (c. 55–30 Ma), respectively. The average cooling rates were 1.05 °C/Myr and 0.93 °C/Myr, respectively, corresponding to average denudation rates of 42 m/Ma and 37 m/Ma. These two episodes of rapid uplift are corresponding to tectonic events on the southwestern margin of the Yangtze Plate during the Indosinian Orogeny, and the collision between the Eurasian and Indian Plates during the Himalayan Orogeny.