The giant Gejiu ore field, located in the southeastern Yunnan Province, China, developed a large-scale Sn–Cu mineralization related to the Cretaceous felsic–mafic magmatism. However, the genesis of Cretaceous mafic–intermediate intrusions remains controversial, which limits our understanding of the Cu source, Sn–Cu symbiotic mechanism, and geodynamic setting of the Gejiu region. To elucidate these issues, we conducted geochronological and geochemical evaluations on the Gejiu mafic–intermediate intrusions, including gabbro, syenite, and monzonite. The mafic–intermediate intrusions formed in 82.1–83.8 Ma, which are contemporaneous with ore-forming granites and ore bodies within the error range. Combined with the cumulus texture in gabbro, linear or parallel elemental plots, and similar and enriched Sr–Nd–Hf isotopes ((87Sr/86Sr)I = 0.708870–0.709811; εNd(t) = − 5.24–−7.70; εHf(t) = − 4.8–2.5), the gradually increased Sr isotopes from gabbro through syenite to monzonite indicated that the Gejiu mafic–intermediate intrusions were formed by fractional crystallization and varying degrees of crustal assimilation of partial melts of an enriched lithospheric mantle.Based on the above research, we compiled geochronological and geochemical data of magmatic–metallogenic events in the region. The Sr–Nd isotopic and elemental ratios (i.e., Zr/Hf, Nb/Ta, Rb/Sr and Ba/Rb) of the Gejiu granites are located between the mafic–intermediate intrusions and spatially temporally connected Laojunshan granites, which indicate that the magma mixing between the enriched mantle–derived Cu-rich magma and metasedimentary rock–derived Sn-rich granitic magma generated Sn–Cu-rich granitic magma. This magma then evolved into the giant Gejiu Sn–Cu deposit via crystal fractionation and fluid exsolution. Combined with the regional geological data and spatiotemporal framework of Sn–polymetallic deposits, the magmatic–metallogenic model of the giant Gejiu Sn–Cu ore field further demonstrates that the southwestern slab rollback of the Neo-Tethyan oceanic plate during the Late Cretaceous controlled its formation.