The genesis of the Bangongco-Nujiang metallogenic belt (BNMB), located in the central portion of the Qinghai-Tibet Plateau, is closely related to the tectonic evolution of the Bangongco-Nujiang Ocean. Although the metallogeny of the western and central BNMB is well understood, the eastern part of this belt has not received much attention to date. The Jinmuguo deposit, the subject of this study, is a recently discovered porphyry Mo polymetallic deposit in the eastern BNMB. Here we present the geology, geochronology and isotopic characteristics of this deposit. Zircon U-Pb dating of the ore-related granite porphyry yielded an age of 118.6 ± 0.7 Ma (n = 20) whilst Re-Os analyses of molybdenite constrain the timing of mineralization as 117.9 ± 2.4 Ma (n = 4). These new age data suggest that magmatism and mineralization were coeval during early Cretaceous. In addition, the S isotope values of sulfide minerals from the Jinmuguo deposit show a narrow range of 2‰ to 4‰, suggesting a magmatic sulfur source. The Pb isotopic character of sulfides indicates a heterogenous lead source. Whilster the H-O isotopic composition (δD values −84.8‰ to −69.1‰, δ¹⁸O_H2O values 4.2‰ to 4.7‰) is consistent with a dominantly magmatic hydrothermal fluid. Overall, our study of the mineralization and alteration characteristics suggests that the Jinmuguo deposit is a porphyry Mo polymetallic deposit related to early Cretaceous felsic magmatism. A comparison of the latter with the other deposits of the BNMB suggests that the entire belt has potential to host a diverse range of magmatic arc-related mineral deposit types.