Abstract Arc-arc amalgamation occurs during the evolution of composite orogens at convergent plate margins and plays a critical role in controlling accretionary patterns and processes. The eastern Junggar terrane in the southern Central Asian Orogenic Belt underwent a long-lived subduction-accretion process in the Paleozoic, but whether and how the Yemaquan and Dananhu-Harlik arcs were amalgamated remain debatable. A systematic U-Pb–Hf-O isotopic study was conducted on zircons from Silurian granitic rocks in the Yemaquan arc. The U-Pb dating results suggest that these rocks were emplaced at 433–422 Ma and inherited abundant 536–435 Ma zircons representing a predominant magmatic episode in the Yemaquan arc. Their positive εHf(t) values and young Hf model ages indicate that the Yemaquan arc is dominated by juvenile basement with significant crustal growth during the Neoproterozoic to early Paleozoic. The variations in zircon Eu/Eu*, εHf(t), and δ18O values reveal that the Yemaquan arc experienced remarkable crustal thickening and remobilization at ca. 450 Ma, similar to the northern Dananhu-Harlik arc, and this was followed by extension that initiated at ca. 420 Ma. These features support the amalgamation of these two arcs occurring ca. 450–420 Ma. Integrated with regional data, we correlated this amalgamation event in the eastern Junggar terrane with the orogenic event in the Chinese Altai terrane, and we propose a middle Paleozoic tectonic evolution model in the eastern Junggar–Altai area from arc assembly to dispersal in association with a transition in accretionary mode. This scenario probably took place as a response to plate reorganization during the breakup of the northern margin of Gondwana.