The Yingqian uranium deposit in the Taoshan-Zhuguang belt, South China is a typical granite-type uranium deposit. The geological characteristics and timing of mineralization are not clear, which hinders the understanding of the ore genesis of the Yingqian deposit as well as regional uranium metallogeny in the Taoshan-Zhuguang belt. These scientific problems are examined in this study through detailed field work and petrographic study, as well as geochemical and geochronological analyses on apatite, rutile and zircon. The orebodies of the Yingqian uranium deposit are mostly present in the medium–coarse grained biotite granite and fine grained two-mica granite, and controlled by the NE-trending faults. The principle U-bearing minerals are pitchblende and brannerite, with the presence of metal minerals like pyrite, hematite and minor galena and sphalerite. The predominant hydrothermal alterations are hematitization, fluoritization, illitization, silicification, chloritization and carbonatization. Gangue minerals are mainly quartz, fluorite, illite and calcite. Moreover, four hydrothermal stages can be recognized in the Yingqian deposit, and the second and third stages are the uraniferous ones. The alterations and mineral assemblages indicate ore fluids are acidic, oxidized, and rich in F, P, CO2, which is favorable for dissolving uranium. Abundant apatite and rutile are discovered in the uraniferous third-stage veins. Geochemical analyses indicate that rutile is plotted in the hydrothermal area in the Ti-100 (Fe + Cr + V)-1000 (W) ternary diagram, and apatite is classified as fluorapatite. In-situ LA-ICP-MS dating indicates that the ore-hosting medium–coarse grained biotite granite and fine grained two-mica granite obtain the zircon U-Pb ages of 160.0 ± 0.3 Ma and 164.1 ± 0.6 Ma, which are consistent with many Jurassic granites in the South China Block. The hydrothermal apatite and rutile yield the U-Pb ages of 96.4 ± 11.6 Ma and 85.6 ± 10.8 Ma, respectively, indicating that uranium mineralization is significantly younger than the ore-hosting granites and generally coeval with the regional mafic magmatism. Consequently, the uraniferous fluids in the Yingqian deposit are independent from the magmatic system. Combined with previous research, it is concluded that fluid convection promoted by mantle–crust interaction would leach uranium from various lithologies, and fluid-rock interactions, fluid boiling and cooling are the causes for uranium precipitation.