The East Qinling Orogen as an important segment of central China that records a complex tectonic evolution history. The Huangbeiling pluton is a rare S-type granite in this orogen and has vital significance in understanding the tectonic evolution of the Qinling Orogen during the Late Mesozoic. The biotite monzogranite of this pluton is the major ore-hosting rocks of the Yumugou Mo-W deposit. In this study, we newly reported a muscovite monzogranite and conducted detailed petrological, geochemical (whole-rock, biotite, muscovite major and trace elements), and zircon U-Pb dating investigations on both the biotite and muscovite monzogranites from the Huangbeiling pluton, with a view to reveal their physico-chemical conditions of formation, petrogenesis and tectonic evolution. Zircon U-Pb dating yielded a weighted mean 206Pb/238U age of 126.8 ± 0.6 Ma for muscovite monzogranite, integrated with published zircon U-Pb age (156–132 Ma) of biotite monzogranite, indicating that the Huangbeiling pluton was produced by two episodes of magmatism during the Late Mesozoic. The pluton shows formation temperatures in the range of 670–772°C, and is classified as cold granites that formed in a subduction-related setting. The emplacement depth of Huangbeiling pluton is constrained at ca. 0.3–4.6 km, with an average depth of 2.0 km. The biotite monzogranite has higher oxygen and fluorine fugacities than the muscovite monzogranite, suggesting high potential for Mo mineralization. Geochemically, the muscovite monzogranite is identified as a S-type granite sourced from crust-derived clay-rich mudstone, and underwent muscovite dehydration melting and subsequent fractional crystallization of K-feldspar and plagioclase during magma ascend. In combination with the syn- to post-collision geochemical affinities of the Huangbeiling pluton and the Late Mesozoic tectonic evolution of the Qinling Orogen, we propose two episodes of magmatism in the Huangbeiling pluton during the tectonic transition (150–125 Ma) from compression to extension in the Qinling Orogen. The first episode (156–132 Ma) of magmatism is correlated with the delamination of lithospheric mantle and intra-continental subduction of the North China Craton under compressional tectonics, whereas the second episode (∼126 Ma) of magmatism occurred through muscovite dehydration melting during pressure decrease.