The Waifangshan Mo-quartz vein cluster occurs at the northernmost margin of the Qinling Orogen. The orebodies occur as quartz veins and are controlled by low-angle faults. We identify three hydrothermal stages, characterized by veinlets of quartz–pyrite, quartz–molybdenite–pyrite–chalcopyrite–galena–sphalerite, and quartz–carbonate assemblages, respectively. The early-stage quartz veins were structurally-deformed, brecciated, and filled by non-deformed middle- or late-stage veinlets, suggesting that the mineralization is associated with a tectonic transition from compression to extension. Five molybdenite separates from the Zhifang Mo deposit yield individual Re–Os ages from 241.2 ± 1.6 to 247.4 ± 2.5 Ma, with a weighted mean age of 243.8 ± 2.8 Ma. Individual Re–Os isotope ages of four molybdenite samples from the Badaogou Mo deposit range from 238.9 ± 2.1 to 255.8 ± 2.2 Ma, with a weighted mean age of 246 ± 10 Ma. Four analyses of molybdenite separates from the Xiangchungou Mo deposit yield individual Re–Os isotope ages of 243.8 ± 8.8 to 247.7 ± 4.4 Ma, with a weighted mean age of 246.0 ± 1.1 Ma. All of these data yield a weighted mean age of 241.9 ± 1.9 Ma, coeval with the accretionary orogeny. We thus conclude that the Waifangshan Mo-quartz veins formed during a transition from continental arc to back-arc setting. The Waifangshan Mo-quartz veins share similar geological, geochemical and geochronological features with the orogenic-type systems. We propose that the Waifangshan Mo-quartz veins are an orogenic-type Mo mineralization, and possibly represent the deepest member in the crustal continuum model of the orogenic-type mineral systems. The molybdenite samples from the Mo-quartz veins in the Waifangshan area have low Re contents (1.457 to 39.16 ppm), suggesting a continental crust-dominated source.