The Xing–Mong Orogenic Belt (XMOB) is located in the eastern part of the Central Asian Orogenic Belt (CAOB) and has experienced multiple tectonic events. The Baiyinnuoer Pb-Zn deposit may be a rare case that documents two periods of mineralization in the tectonically complex XMOB. There are two types of Pb-Zn mineralization in the deposit: (1) skarn-type ore, hosted by the skarn in the contact zone between marble and granodiorite and within the marble and (2) vein-type ore, hosted by crystal tuff and feldspar porphyry. This study revealed that the host rocks, mineral assemblages, mineralization occurrences, S-Pb isotopes, and ages between the two types of ore are notably different. Zircon U-Pb dating indicates that the granodiorite was emplaced in the Early Triassic (244 ± 1 to 242 ± 1 Ma), the crystal tuff was deposited in the Early Cretaceous (140 ± 1 to 136 ± 1 Ma), and the feldspar porphyry was intruded in the Early Cretaceous (138 ± 2 to 136 ± 2 Ma). The first skarn mineralization occurred at ∼240 Ma and the second vein-type Pb-Zn mineralization took place between 136 and 129 Ma. Thus the Triassic orebodies were overprinted by Early Cretaceous mineralization. The sphalerite and galena from the skarn mineralization have higher δ34S values (−4.7 to +0.3‰) than the sphalerite, galena and aresenopyrite from the vein-type mineralization (−7.5 to −4.2‰), indicating different sulfur sources or ore-forming processes for the two types of mineralization. The Pb isotopic compositions of the two types of ore are very similar, suggesting similar lead sources. Geochemistry and Nd-Pb-Hf isotopic systematics of the igneous rocks in the region show that the Triassic granodiorite was generated from hybridization of mafic and felsic magmas due to strong crust-mantle interaction under the collisional setting that resulted following the closure of the Paleo-Asian Ocean and the collision of North China and Siberian cratons at the end of the Permian; while the Cretaceous igneous rocks at Baiyinnuoer originated from the partial melting of a juvenile lower crust with minor input from the crust caused by the underplating of mafic magma in an extensional setting.