Convergent plate margins represent an ideal setting to understand the formation and evolution of the Earth's crust. Nevertheless, the geodynamic processes involved in crustal evolution remains highly debatable. Based on a large geochemical dataset of Permian-Cretaceous granitic rocks from the Yanbian area in NE China, we propose a new geodynamic model involving crustal replacement to decipher crustal evolution during a superimposed, multi-stage, subduction system. These Phanerozoic granitic rocks, from two adjacent zones, show contrasting HfNd isotopic variation trends. With decreasing age of magmatism, whole-rock εNd(t) and zircon εHf(t) decrease gradually in the North Granite Zone (NGZ) but show the opposite trends in the South Granite Zone (SGZ). Zircon δ18O shows a slight rise in the NGZ, but it initially increases from Permian to Jurassic and then decreases to Cretaceous in the SGZ. The Nd-Hf-O isotopic compositions of the Cretaceous granitic rocks in both zones converge. Four crustal components are identified in the source of granites across the Yanbian area, including (1) “juvenile” crust, (2) subduction-accretionary complex, (3) new arc crust, and (4) Precambrian crust.The contributions made to the bulk crustal melting source of granites by the “juvenile” crust component in the NGZ and by the Precambrian crust in the SGZ were both gradually decreased, whereas the proportion of the new arc crust increased in both zones. Pre-existing crustal components were extensively eroded, destructed, diluted and replaced by the new arc crust formed during paleo-Pacific slab subduction. Considering the prevalence of these two Nd-Hf-O isotopic variation trends in many orogenic belts, subduction-induced crustal replacement represents an important mechanism for crustal evolution in convergent plate margins.