It is a central issue to eliminate radioactive uranium (U(VI)) efficiently from water. In this manuscript, β-cyclodextrin was cross-linked with 2,3,5,6-tetrafluoro-1,4-benzenedicarbonitrile, and then a carboxylation reaction was used to prepare porous cross-linked polymers rich in carboxyl groups (CA-PCDPs). Subsequently, magnetic nanoparticles (MNPs) were loaded onto the CA-PCDPs via coprecipitation, and magnetic porous β-cyclodextrin polymer nanoparticles (CA-PCDP@MNPs) were successfully obtained, which were used for efficient elimination of U(VI) from nuclear wastewater solution. Moreover, SEM, FTIR, VSM, BET, and XRD were employed to investigate the CA-PCDP@MNP and found that it had a well-developed porous structure, high specific surface area, and abundant oxygen-containing functional groups (carboxyl, hydroxyl, C-O-C, Fe-O, etc.), providing sufficient active sites for chelating uranyl ions. Experiments illustrated that the CA-PCDP@MNP had efficient removal ability for U(VI), and the maximum theoretical adsorption amount for U(VI) reached 245.66 mg/g at pH 6.0 and 303 K. Moreover, the adsorption process was more suitable for the quasi second-order kinetic model and Langmuir adsorption isotherm model, indicating that the adsorption process was chemical adsorption. Meanwhile, the CA-PCDP@MNPs also exhibited fast response magnetic recovery ability and excellent regeneration and recycling ability. In addition, the data of the adsorption mechanism demonstrated that oxygen-containing functional groups, which were rich on the surface of CA-PCDP@MNPs, were the main binding active sites of U(VI). From the above results, it can be deduced that the CA-PCDP@MNP has a good application prospect in the practical application of nuclear wastewater treatment.