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A new fluorescence sensor (QDs-IIP), based on ion-imprinted polymers (IIP) as recognition element and Mn-doped ZnS quantum dots (QDs) as fluorophore, was synthesized for the selective and sensitive determination of hexavalent chromium (Cr(VI)) ions. The QD was first coated by SiO2 layer, and then modified with Cr(VI)-imprinted polymer. Several parameters affecting fluorescence intensity such as tetraethylorthosilicate (TEOS) volume, ZnS:Mn@SiO2 amount, and radiation time were investigated and optimized. The QDs-IIP was characterized by X-ray diffraction (XRD), Fourier transform infrared (FTIR), transmission electron microscope (TEM), and scanning electron microscope (SEM). Furthermore, the fluorescence quenching mechanism was investigated by using UV-VIS and fluorescence spectrophotometer, and it was found that internal filtration effect was the main fluorescence quenching mechanism. The relative fluorescence intensity (F0/F) increased linearly with the increase of Cr(VI) concentration in the range of 20 μg L−1–1.0 mg L−1. The QDs-IIP sensor showed high recognition selectivity for Cr(VI) in comparison with the QDs-NIP sensor with an imprinting factor (IF) of 2.53, and it could be reused 5 times. In addition, an analytical method of Cr(VI) based on the QDs-IIP sensor was established with a limit of detection of 5.48 μg L−1, and was then applied to actual water samples with satisfactory results. Therefore, QDs-IIP can be deemed as a practicable fluorescent sensor for trace Cr(VI) detection. [ABSTRACT FROM AUTHOR]