The novel Cr(VI) anion-imprinted polymer (Cr(VI)-IIP) was prepared by a surface imprinting technique with bifunctional monomers pre-assembly system based on mesoporous silicon (SBA-15). The synthesized Cr(VI)-IIP was characterized by Fourier transmission infrared spectra (FT-IR), energy dispersive spectrometer (EDS), scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray powder diffractometer, N2 adsorption-desorption and thermogravimetric analysis (TGA), proving to be with a highly ordered mesoporous structure, as well as favorable thermal stability. The saturated adsorption amount was 96.32 mg/g, which was 2.7 times higher than that of non-imprinted polymer (NIP). Kinetic experiments showed that the adsorption equilibrium state was obtained within 70 min. In addition, in the selectivity experiments, Cr(VI)-IIP exhibited strong specific recognition ability for Cr(VI) and could realize the separation of Cr(VI) and Cr(III) from an aqueous solution. The dynamic adsorption experiments exhibited that the dynamic adsorption efficiency of Cr(VI)-IIP was as high as 71.57%. Meanwhile, the dynamic regeneration experiments showed that the adsorption amount of Cr(VI)-IIP did not decrease significantly after repeating for five times. All of the findings suggested that Cr(VI)-IIP could achieve precise identification as well as efficient separation of Cr(VI) from aqueous solution.