In this study, the incorporation of U(VI) into CaCO3 under different aging times and U(VI) concentrations was studied by combining batch experiments, X-ray diffraction (XRD), attenuated total reflection Fourier transformed infrared spectroscopy (ATR-FTIR), and extended X-ray absorption fine structure (EXAFS) approaches. Batch sorption experiments showed that the sorption of U(VI) on calcite was strong pH-dependence, and high pH was beneficial for U(VI) sorption possibly due to the electrostatic attraction between positively charged calcite and negatively charged uranyl tri-carbonate species. XRD patterns showed that the [104] facet of calcite shifted toward low angle at pH ∼10.0, which indicated that the uranyl tri-carbonate species of U(VI) possibly diffused into calcite lattice by replacing Ca atoms, and then induced the expansion of calcite crystal cell. The incorporation of U(VI) into CaCO3 showed that the uptake of U(VI) gradually decreased within the first 200 h, and then significantly increased with the increasing aging time. U(VI) incorporation into CaCO3 might experience vaterite, transition from vaterite to calcite, and calcite stages, which were confirmed by XRD, ATR-FTIR, and X-ray absorption near-edge structure (XANES) spectroscopy. As the U(VI) concentration increased, the transition time from vaterite to calcite correspondingly increased, indicating that U(VI) incorporation into CaCO3 can stabilize vaterite phase. EXAFS analyses suggested that the local structure of uranyl moiety was changing during the incorporation process, and the species of U(VI) incorporation into vaterite was similar to uranyl carbonates, however indeed different from the species of uranyl tri-carbonate presented in calcite.