The petrogenesis of continental arc magmas provides critical insights into thermal evolution and geodynamics of the continental lithosphere, crust-mantle interaction, and deep dynamic processes. In this study, we report new zircon U-Pb ages along with isotopic and elemental whole-rock geochemistry, mineral chemistry, and Hf-O isotope data for the Kalaqigu diorites and monzogranites of the Chinese Wakhan Corridor, South Pamir. Zircon U-Pb dating indicates that the Kalaqigu pluton was emplaced in the Early Cretaceous (ca. 108−106 Ma). The diorites are geochemically characterized by low SiO2 (51.9−54.5 wt%) and CaO (7.7−9.4 wt%) contents, but high MgO (5.3−8.3 wt%), Al2O3 (12.8−16.8 wt%), and TiO2 (0.6−1.1 wt%) contents as well as high Mg# (56−65) values. Thus, they are similar to high-Mg diorites: enriched in large ion lithophile elements (e.g., K, Sr, and Ba) and light rare earth elements, while depleted in high field strength elements (i.e., Nb, Ta, Zr, and Hf). Combined with negative εNd(t) (−6.9 to −14.0) and εHf(t) (−9.9 to −12.2), and high (87Sr/86Sr)i (0.7075−0.7086) ratios, these observations indicate that they originated from an enriched lithospheric mantle source. High δ18Ozrn (7.49‰−9.01‰) values, in conjunction with relatively high 207Pb/206Pb and 208Pb/206Pb ratios, suggest that the source was modified by subducted sediment-derived melts. Variable Cr contents (54−117 ppm) are likely controlled by minor fractionation of olivine and orthopyroxene. The monzogranites show high SiO2 contents (69.2−72.0 wt%), and low Rb/Sr (0.4−0.6), (K2O + Na2O)/CaO (2.6−4.8), and FeOT/MgO ratios (2.6−3.2). They contain diagnostic cordierite and show strongly peraluminous characteristics (A/CNK > 1.1) with high δ18Ozrn (7.82‰−8.85‰) values that are compatible with those of typical S-type granites. Their abundant inherited zircons, with age populations similar to those of detrital zircons from regional early Paleozoic metasedimentary rocks, indicate that they were derived from partial melting of ancient metasedimentary rocks. Phase equilibrium modeling is consistent with biotite-dehydration melting of metagreywacke, probably at ∼750 °C and ∼6.0 kbar, as indicated by the biotite chemistry. Based on regional geochronology, a south-to-north magmatic migration suggests that northward flat-slab subduction of the Neo-Tethyan oceanic slab played an important role in the generation of these widespread Early Cretaceous continental arc magmatic rocks. However, the granitoids were generated earlier than the mantle-derived mafic rocks, which suggests that crustal melting occurred during the early stage of subduction. The continuous flat-subduction resulted in partial melting of subducted sediments, which metasomatized the mantle wedge. Contemporaneous regional compression primarily occurred far north of the subduction zone (i.e., North and Central Pamir), inducing deformation as well as crustal shortening. With the flare-up of continental arc magmatism in South Pamir, crustal shortening moved southward. These processes, combined with the addition of voluminous, mantle-derived magmas, played an important role in crustal thickening in Pamir during the Early Cretaceous.