The Sanjiang Tethyan Metallogenic Domain (STMD) is an important part of the Tethyan giant metallogenic belt. The Yidun Arc is a part of the STMD in the eastern Tibetan Plateau. Recently, four newly discovered Mo–Cu–(W) ore deposits related to granitic intrusions were found distributed along the north-south strike in the southern Yidun Arc, which are identified as the Xiuwacu, Relin, Hongshan, and Tongchanggou deposits herein. These four deposits formed along high-angle north-northwest or north-west strike-slip faults, with vein-type and porphyry-type Mo–Cu mineralization developed in the intrusions. Molybdenite Re–Os and zircon U–Pb dating together with zircon Hf isotopes and whole-rock geochemistry of the intrusions were studied to discern the relationship between mineralization and magmatism, metallogenesis, and tectonic settings. Molybdenite from skarn-type mineralization at the Hongshan deposit has a Re–Os isochron age of 81.2 ± 2.6 Ma (MSWD = 1.3, n = 5) consistent with previously published zircon U–Pb ages and Re–Os ages of porphyry-type Mo mineralization. These results indicate that the Hongshan is a Late Cretaceous porphyry-skarn Cu–Mo deposit. Zircon U–Pb ages of the granitic intrusions in the Xiuwacu, Relin, and Tongchanggou deposits varying from ~ 87.4 Ma to ~ 82.7 Ma. Combined with published molybdenite Re–Os age spectrum (~ 85 Ma to ~ 81.2 Ma), it is proposed that the Mo–Cu–(W) mineralization in the Shangri-La region is spatially, temporally, and probably genetically related to the Late Cretaceous granitic intrusions. The Relin, Hongshan, and Tongchanggou intrusions have high SiO₂ (65.2–70.0 wt.%), Sr (363–905 ppm), Sr/Y (22–72), and La/Yb (37–69) ratios, and low Y (11.6–17.0 ppm) and Yb (0.97–1.59 ppm), which displayed adakitic affinities. Their low MgO (0.66–1.44 wt.%), Mg# (25–46), variable negative zircon ε_Hf(t) values (− 7.9 to − 2.3), and Proterozoic two-stages Hf model ages (T_DM2 = 1.13–1.62 Ga) suggest that they were probably dominantly derived from partial melting of thickened lower continental crust. According to the tectonic evolution of the Bangong Meso-Tethys Ocean during the Late Mesozoic, the Late Cretaceous igneous event and mineralization in the Yidun Arc likely formed under a late- or post-collision extensional environment, probably related to the collision between the Lhasa and Qiangtang terranes during the Late Cretaceous.