The Zhunsujihua porphyry molybdenum deposit, located in northern Inner Mongolia of China that belongs to Central-Asian Orogenic Belt (CAOB), is the only Mo deposit formed in the late Carboniferous in this area so far. Its mineralization is mainly restricted to the Zhunsujihua granitoid intrusions, which are composed of the main granodiorite (GD) and crosscutting, virtually coeval minor syn-ore leucogranite (LG) and diorite porphyry (DP) dykes. LA-ICP-MS zircon U–Pb dating yields crystallization ages of 300.0 ± 2.0, 299.3 ± 2.0, and 299.0 ± 2.6 Ma for the GD, LG, and DP, respectively. The major and trace element lithogeochemical data show that the GD and LG are metaluminous to weakly peraluminous, high-K calc-alkaline series with I-type granite characteristics, strongly oxidized, with low concentrations of Ba, Nb, Sr, P, and Ti and elevated K and Rb contents, indicating typical arc magmatic features. The LG is a product derived by extensive fractional crystallization of a parental magma similar to the GD as evident from the lower Eu/Eu*, Nb/Ta, Zr/Hf, and T Zr. The moderately altered DP exhibits high concentrations of K, Rb, Cs, LREE, Y, and low Sr/Y, with a positive e Nd (300 Ma), which indicates a mantle or juvenile source associated with an arc setting. The Sr–Nd–Hf isotope data show low I Sr (0.70406–0.70461) and moderate e Nd (300 Ma) (−0.9 to 1.5) for the GD and LG, and relatively high e Hf (300 Ma) values (−3.6 to +11.2) for the GD, suggesting the magma mainly originated from the juvenile lower crust that was derived from depleted mantle, with a minor component of ancient continental crust. Lead isotope data have characteristics of a lower crust source with minor contamination by upper crustal material. Combined with previous research, the Zhunsujihua granitoid intrusions developed in an intracontinental volcanic arc (Uliastai) associated with northward subduction of the Paleo-Asian Ocean plate during late Carboniferous to early Permian; this suggests that the subduction of Paleo Asian Ocean may have continued to late Carboniferous, and the Hengenshan basin is probably closed during the early Permian. Fractional crystallization is the main evolutionary process of the felsic magma, which has played an important role in the Mo mineralization. The coeval DP may have provided additional heat for the extended evolution of the crystallizing felsic magma chamber.