The recently-discovered Wenquan porphyry Mo deposit hosted in the Wenquan granite of the West Qinling Orogen has been recognized as a product of the Indosinian metallogenesis. Three generations of mineral assemblage for the deposit are identified as follows: (1) quartz–biotite–K-feldspar; (2) quartz–sulfide and (3) sulfide–calcite. Geochemical study shows that the mafic microgranular enclaves(MMEs) in the ore-bearing Wenquan granite have lower SiO₂, and higher Mg# and Nb/Ta ratios than the host granite itself. Different from the granite which have zircon ε_Hf(t) values of − 3.6–3.0 and T_DM2 of 1234–890 Ma, the MMEs are characterized by the ε_Hf(t) values of − 10.1–10.8 and T_DM1 of 865–441 Ma. This can be interpreted to indicate a mixture origin of the Meso- and Neoproterozoic crust-derived component and Neoproterozoic SCLM-derived materials for the formation of the Wenquan granite, which played an essential role in the Mo mineralization. Comparative Pb isotopic data between ores and K-feldspar suggest that the Wenquan granitic magma originated from the middle-lower crust of the South China Block and the ore-forming materials were incorporated by hydrothermal fluid differentiated from the Triassic magmatic system, with minor contribution of sedimentary rocks. The δ³⁴S values of 5.0–11.7‰ with a pronounced mode at 5.0 to 6.1‰ for the ores probably represent the sulfur incorporation of a typical magmatic hydrothermal fluid contaminated by heavy sulfur of Devonian sediments. The granite yielded the zircon U–Pb ages of 218 ± 2.4 Ma and 221 ± 1.3 Ma, as the same as the ages of 217 ± 2.0 Ma and 218 ± 2.5 Ma obtained for the MMEs. These ages are indistinguishable with the molybdenite Re–Os isochron age of 219 ± 5.2 Ma which is the timing for the Mo mineralization. Tectonically, the magmatic mixture processes of the Wenquan granite and the Mo mineralization to form the Wenquan Mo deposit contemporaneously occurred during the transition of tectonic regime from syn- to post-collision orogeny in the Qinling Orogen in the Late Triassic.