The Pamir orogen originated through the amalgamation of various arc terranes. Despite undergoing numerous studies, the subduction polarity and time regarding the accretion processes remain inadequately constrained. To address these issues, we carried out a detailed study of zircon and apatite U-Pb ages, zircon Hf isotopes, and whole-rock geochemistry for the Permian to Cretaceous gabbro, volcanic rocks and granitoids from the Southern Pamir and the Rushan-Pshart suture. Three stages of magmatism are identified, including 279–266 Ma gabbro and andesite to dacite, 209–208 Ma granitoids, and 108–103 Ma gabbro and granitoids, respectively. The Permian gabbro and basaltic andesite to dacite in Pshart Range are enriched in light rare earth elements (LREE) and large ion lithophile elements (LILE), but are depleted in Ta, Nb, and Ti, suggesting formation from an enriched mantle source in a subduction zone. The Late Triassic I-type granitoids are typical arc calc-alkaline magmatic rocks with εHf(t) values varying from −8.7 to −3.5, which mainly sourced from the partial melting of mixed crustal sources predominately consisting mafic rocks with minor metasedimentary rocks. The Early Cretaceous Pshart granites are I-type granites with relatively low εHf(t) values ranging from −14.6 to −2.9, suggesting that they were crust-derived rocks. The Early Cretaceous Bazardara granites are identified as A2-type granites with the εHf(t) values ranging from −18.3 to +5.3, and were derived from mixing of mantle-derived and crust-derived magmas, or interaction between mantle melts and old crustal rocks. The early Cretaceous gabbro exhibits -MORB-like geochemical characteristics with flat REE pattern (La/YbN = 4.96), moderate enrichment of LILEs and weak depletion of Nb, Ta and Ti (Nb/LaPM = 0.94). Thus, the early Cretaceous A2-type granite, E-MORB-like gabbro and volcanic rocks were formed in an extensional setting. Our new data indicate that the southward subduction of the Rushan-Pshart oceanic slab started in the Early Permian and continued to the Late Triassic. Moreover, combining the previous data, we conclude that the Early Cretaceous granites and gabbro in the Southern Pamir formed in an extensional environment due to the southward rollback after northward near-flat subduction of the Neo-Tethyan oceanic lithosphere. Display omitted •Permian, Triassic, and Cretaceous arc rocks are identified in the South Pamir.•Southward subduction of the Rushan-Pshart Ocean began before the Permian.•The southward subduction formed the late Triassic I-type granites.•Slab roll-back of the Shyok Ocean caused within-plate magmatism in the South Pamir.