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An integrated study using cathodoluminescence (CL) images, U–Pb geochronology, and Hf isotopic characterization of zircons was performed on migmatites from the Yuka terrane to provide insights into the timing and nature of the protoliths, metamorphism, and partial melting of these rocks. Zircon grains separated from the migmatites have three distinct domains. Residual zircon cores in samples YKT01 and YKT02 exhibit oscillatory zoning, high Th/U ratios (0.10–0.79), steep heavy rare earth element (HREE) patterns, and mean ages of 936 ± 5 Ma and 927 ± 11 Ma, respectively, indicating that they are igneous in origin and record Neoproterozoic magmatism during the Grenvillian Orogeny. CL‐grey cores record an ultrahigh‐pressure (UHP) peak metamorphism age of 435 ± 5 Ma and have low Th/U and 176Lu/177Hf ratios, weak negative Eu anomalies, and relatively flat HREE patterns. The CL‐bright rims have steep HREE patterns with lower middle rare earth element (MREE) concentrations but higher HREE concentrations compared with the metamorphic cores and a weighted average age of 422 ± 4 Ma, which records the timing of melt crystallization. The migmatites incorporate garnet relicts coexisting with fluid inclusions and hydrous minerals like peritectic phengite and peritectic large anhedral poikilitic tourmaline in the leucosomes. Peak temperatures are less than 750°C, suggesting that the anatectic melts may be derived from melting of felsic gneiss in the presence of water. The timing of melt crystallization is ca. 13 Ma later than UHP metamorphism, indicating that the partial melting took place during the exhumation stage. The metamorphic zircon cores have higher 176Hf/177Hf(t) ratios than the residual magmatic cores, which provides powerful evidence for the generation of the metamorphic zircons through the incorporation of internal high Hf minerals other than zircon in a closed system. Anatectic rims with lower 176Hf/177Hf(t) ratios but higher 176Lu/177Hf ratios than metamorphic cores suggest that the main formation mechanism is dissolution‐reprecipitation of pre‐existing zircons. In conclusion, the elevated 176Hf/177Hf(t), TDM2 age and decreasing 176Lu/177Hf(t) ratios in the metamorphic and anatectic domains imply that the new zircons in some migmatites and granites may not reflect the Hf isotope compositions of their source rocks, accounting for the variable Hf isotope compositions in S‐type granites. [ABSTRACT FROM AUTHOR]