The Qinxi silver deposit is located in eastern Fujian Province, South China. It is hosted in the late Jurassic Nanyuan volcanic unit and controlled spatially by structural alteration zone. The origins of the deposit are understood poorly. In this study, systematic field geology, precise sulfide geochronology, and H–O–S–Pb isotope analyses were carried out. The symbiotic minerals and ore assemblages are interpreted as evidence that Qinxi ore is a typical middle to low temperature hydrothermal deposit. Galena and sphalerite from the ore yield a Rb–Sr isochronal age of 130 ± 2.0 Ma (MSWD = 1.7), and single galena samples yield a Rb–Sr isochronal age of 130 ± 7.1 Ma (MSWD = 2) and are evidence that the ore was formed in the early Cretaceous period. The silver-bearing quartz vein has O:H and 18O:16O ratios intermediately between magmatic and meteoric water (δ18 Owater-smow from −2.50‰ to −0.1‰ and δDv-smow from −73.6‰ to −60.7‰). The δ34 S values of metal sulfide are close to the primitive mantle sulfur values (δ34S = −1.7 to 7.1‰, avg. = 0.92‰). The Pb isotopic compositions from the ore are similar to those of the hosted volcanic unit, with a value between the upper crust and mantle isotope composition (206Pb/204Pb = 18.421~18.605, 207Pb/204Pb = 15.580~15.772, 208Pb/204Pb = 38.591~39.183). Lead–zinc sulfides have mature crustal-derived Sr isotopic features ((87Sr/86Sr)i = 0.7103). Thus, the metallogenic source materials mainly came from the crust. Moreover, regional geological studies suggest that the Qinxi ore deposit was likely formed in an extensional terrane.