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Zircons widely occur in magmatic rocks and often display internal zonation finely recording the magmatic history. Here, we presented in situ high-precision (2SD <0.15‰ for δ 94 Zr) and high–spatial-resolution (20 µm) stable Zr isotope compositions of magmatic zircons in a suite of calc-alkaline plutonic rocks from the juvenile part of the Gangdese arc, southern Tibet. These zircon grains are internally zoned with Zr isotopically light cores and increasingly heavier rims. Our data suggest the preferential incorporation of lighter Zr isotopes in zircon from the melt, which would drive the residual melt to heavier values. The Rayleigh distillation model can well explain the observed internal zoning in single zircon grains, and the best-fit models gave average zircon–melt fractionation factors for each sample ranging from 0.99955 to 0.99988. The average fractionation factors are positively correlated with the median Ti-in-zircon temperatures, indicating a strong temperature dependence of Zr isotopic fractionation. The results demonstrate that in situ Zr isotope analyses would be another powerful contribution to the geochemical toolbox related to zircon. The findings of this study solve the fundamental issue on how zircon fractionates Zr isotopes in calc-alkaline magmas, the major type of magmas that led to forming continental crust over time. The results also show the great potential of stable Zr isotopes in tracing magmatic thermal and chemical evolution and thus possibly continental crustal differentiation.