The Yaolinghe Group in the central part of the Qinling Mountains includes Neoproterozoic bimodal volcanic and sedimentary sequences and two units with fault contact can be divided. The lower unit consists of bimodal volcanic and sedimentary rocks intruded by a coeval plutonic complex, granitic dikes and small granitic bodies, and the upper unit is made up of greenschist with minor rhyolitic tuff. Zircon U–Pb dating yields ages of 719–790Ma for meta-rhyolitic tuff in the lower unit, 714–721Ma for the intrusive rocks, and 635Ma for meta-rhyolitic tuff in the upper unit. The δ 18 O values are −4 to 15‰ for whole-rock, quartz and zircon from the volcanic rocks and quartz veins in the lower unit and the intrusive rocks, and 3.4–12‰ for whole-rock and quartz veins in the upper unit. Low to negative δ 18 O values (−4 to 4‰) are widely present in the rocks and quartz veins of the lower unit and the intrusive rocks, suggesting that the lower unit and the intrusive rocks suffered meteoric fluids-in hydrothermal alteration. The δ 18 O values of whole-rock and quartz veins in the upper unit do not exhibit striking 18 O depletion, indicating that meteoric fluids-in hydrothermal alteration did not occur in this unit. Low δ 18 O zircon grains (1–4‰) are common in some of meta-rhyolitic tuffaceous and intrusive rocks, and only two analyses have negative δ 18 O values. The low δ 18 O values of zircon were inherited from crystallization of low δ 18 O magma, which was formed through the remelting of previous magmatic rocks altered by meteoric water in a system of magma chamber-caldera, and weakly affected by meteoric fluid-in hydrothermal alteration. Thus the presence of low δ 18 O magmatic zircon is an indicator for meteoric fluid-in hydrothermal alteration. The low δ 18 O zircon grains found in different samples yields the ages from 720 to 790Ma, implying that meteoric fluid-in hydrothermal alterations began earlier than 790Ma, whereas the striking 18 O depletion of the intrusive rocks suggest that hydrothermal alteration continued to at least 714Ma, and the lack of 18 O depletion in the upper unit constrains that meteoric fluid-in hydrothermal alterations stopped before 635Ma. The long duration of meteoric fluid-in hydrothermal alteration do not support that the glacial meltwater from the Neoproterozoic glaciations in the Yangtze craton is responsible for the 18 O depletion of the rocks.