Most porphyry Cu deposits are formed in magmatic arc settings, but some occur in non-arc environments, such as intracontinental settings. The petrogenesis of fertile magmas for porphyry Cu deposits formed in intracontinental settings is still ambiguous. To address this issue, we performed an integrated study of the late Mesozoic porphyry Cu deposits in the South Qinling Orogenic Belt. Zircon U–Pb ages indicate that these late Mesozoic porphyry Cu deposits were formed at 149–142 Ma, in a postcollisional intracontinental setting. εNd(t) (− 4.5 to − 2.7), initial ⁸⁷Sr/⁸⁶Sr (0.7046 to 0.7084), and zircon εHf(t) values (− 3.8 to + 2.2) of the late Mesozoic ore-forming and barren rocks suggest that both originate from Meso-Neoproterozoic juvenile lower crust. Whole-rock geochemical and isotopic characteristics indicate that the ore-forming rocks could be formed by the delamination of thickened juvenile lower crust or by the reaction of mantle with normal juvenile lower crust. The barren rocks could be formed by the partial melting of thickened or normal juvenile lower crust. Whole-rock petrochemistry and reversed anorthite contents and Sr isotope data of zoned plagioclase crystals indicate that the mafic magma was recharged into the ore-forming magma chamber. Due to the injection of mafic magma, the ore-forming rocks obtained higher oxygen fugacity, volatiles, water, sulfur, and Cu contents than the barren rocks. According to the regional tectonic evolution, the late Mesozoic porphyry Cu deposits in the South Qinling Orogenic Belt were formed in an extensional environment due to transformation of the tectonic regime. Large-scale lithospheric extension caused asthenospheric mantle upwelling and crust-mantle interaction, providing the crucial metallogenic conditions. Moreover, the injection of mantle-derived mafic magma into the normal magma is a key factor in the formation of the late Mesozoic porphyry Cu deposits in the SQB and similar porphyry systems in an intracontinental setting.