Diffusion-driven isotopic fractionation during crystal growth and crystal-melt interaction has important implications for identifying diffusive processes and estimating the timescales of magmatic processes. Especially, Fe-Ti-Cr oxides are common crystalline phases in both relatively unfractionated and highly evolved basaltic magmas and may record the evolution history of the host magmas. High-precision Zn and Mg isotopic compositions for a set of Fe-Ti-Cr oxides and their host lavas in three types of Cenozoic basalts (sodic, transitional and potassic) from northeast China are reported in this study. These oxide crystals exhibit a wide range of chemical compositions (e.g., FeOT = 20.6–49.1 wt%, TiO2 = 1.38–8.70 wt%, Cr2O3 = 16.2–43.1 wt%), reflecting substantial chemical disequilibrium with their host magmas. A large range of δ66ZnJMC-Lyon from −1.12‰ to 0.24‰ and δ26MgDSM-3 from 0.04‰ to 0.80‰ is observed in oxides (n = 17) from all three lava types. Compared with the host basalts, the oxides are enriched in lighter Zn with △66Znoxide-melt (δ66Znoxide–δ66Znmelt) from −1.43‰ to −0.19‰ and heavier Mg with △26Mgoxide-melt (δ26Mgoxide–δ26Mgmelt) from 0.43‰ to 1.13‰. Comparison with existing theoretical work indicates that these isotopic offsets, even if compositional effects of oxides are considered, are too large to be in equilibrium. There are negative correlations between tetrahedral-site Fe2+ + Zn2+ and Mg2+ (R2 = 0.97) and between δ66Zn and δ26Mg (R2 = 0.66) for the oxides, which are best attributed to isotopic fractionation induced by Zn–Mg inter-diffusion, supported by the core-to-rim increase of Zn contents and decline of Mg contents in zoned oxides. Our results thus suggest that inter-diffusion between Mg and Zn can occur during crystal growth and reaction with host magmas, which is commonly observed between Mg and Fe, and this process is accompanied by strong Zn and Mg isotope fractionations. Such fractionations can be utilized to estimate the timescales for the formation of zoned minerals. Numerical simulation yields a short (∼35 days) diffusion interval for the observed Zn and Mg isotopic variations in the investigated oxide crystals, which indicates rapid cooling of the host lavas. Our results also indicate that fractional crystallization of oxides would lead to slight δ66Zn increase and δ26Mg decrease in the residual melts. Such fractionation should be considered while characterizing the Zn and Mg isotopic compositions of evolved magmas with low MgO and Zn contents.