The South China hosts a number of stratiform deposit in Late Paleozoic depression, including the Yushui copper deposit (which has a Cu grade up to 53% with an average grade of about 3.5%) in the Yong-Mei-Hui depression. The genesis type of Yushui copper ore is highly controversial due to the influence of post mineralization tectonic and magmatic activities, which affects the exploration of the deposits. Yushui copper deposit is mainly composed of stratiform ore body and stockwork orebody in the footwall, with typical VMS-type deposit characteristics and its mineralization age of 308 Ma. Small amounts of vein-type ore body can also be seen in the hanging wall dolomite of the stratiform ore body, which mainly develops along the joints and faults, and the mineral assemblage includes chalcopyrite, bornite, galena, sphalerite, tetrahedrite, furutobeite, and rare earth minerals (xenotime and bastnaesite). Hydrothermal sericite is also developed when vein-type ore body cut the sandstone in the footwall of stratiform ore body. Pristine euhedral xenotime and bastnaesite crystals from the Yushui Cu mineralized of veins ore body yield LA-ICP-MS weighted mean 206Pb/238U ages of 162.5 ± 6.7 Ma (1 s, MSWD = 11.8) and 164.6 ± 5.3 Ma (1 s, MSWD = 9.5), respectively. Hydrothermal sericite yields a plateau 40Ar–39Ar age of 163.19 ± 7.60 Ma, which is consistent with the xenotime and bastnaesite U–Pb age, suggesting that the vein-type Cu mineralized is generically related to the Middle-Late Jurassic hydrothermal event. These ages indicate that in addition to the major Late Paleozoic mineralization events that formed VMS-type stratiform ore body, there were also small-scale hydrothermal vein-type ore body formed during the Middle and Late Jurassic mineralization events that did not cause major disruptions to the earlier stratiform ore body. Combining with the chronological research of other copper deposits in the southeastern coastal area of China, this article believes that these 170 ∼ 155 Ma deposits were all due to the crust-mantle interaction caused by changes in the subduction angle of the ancient Pacific plate. Our study suggests that the southeastern margin of the South China has potential for the exploration of polymetallic hydrothermal mineralization related to Middle-Late Jurassic magmatic rock.