Earth’s evolution involves deep, hot rocks rising upward by convection to near-surface environments, as well as the unique scenarios such as the formation and breakup of Gondwana and Pangea. These processes have been well recorded by the widely distributed magmatism. To understand the tectonic evolution and Gondwana assembly, we compiled early Paleozoic zircon U–Pb ages (n = 67), in-situ zircon Hf isotopes (n = 1011), and bulk-rock elemental compositions (n = 293) and Sr–Nd isotopes of magmatic rocks in the Tibetan–Himalayan orogen. Three stages of Paleozoic magmatism were identified here, including early (>490 Ma) to middle (490–470 Ma) to late (<470 Ma) stages, in response to the final assembly of the Gondwana supercontinent. Early-stage magmatic rocks are characterized by highly variable SiO₂ (48.0–80.0 wt%) and MgO (0.02–9.65 wt%) contents with Mg# range from 5.4 to 78, K₂O/Na₂O ratios ranging from 0.14 to 2.81, and whole-rock Sr–Nd (⁸⁷Sr/⁸⁶Sr(i) (0.7035–0.7340), ε_Nd(t) (-9.5–+1.0)) and zircon Hf (ε_Hf(t) = –15 to + 8.0) isotopic compositions with significant mantle contributions; they could be generated in an Andean-type arc setting along the active northern continental Gondwana margin. Middle-stage magmas were dominated by fertile continental crustal signatures (SiO₂ > 70 wt%, A/CNK > 1.10, MgO < 2.69 wt%) in a crustal thickening setting. Late-stage magmas also have highly variable Si, Mg and isotopic components, with coeval mantle-derived magmas developing in an extensive setting. Importantly, the widespread presence of early Cambrian to late Ordovician peraluminous high-K calc-alkaline magmatism in the Tibetan–Himalayan orogen indicates that the reworking of ancient continental crustal materials played a key role in reconstructing and stabilizing the final Gondwana assembly.