Although mesoporous silica with magnetically hybridized two-dimensional channel structures has been well studied in recent years, it remains a challenge to fabricate the counterpart with macroporous three-dimensional cubic structures since the highly acidic preparation conditions lead to dissolution of magnetic particles. Herein, we successfully prepared magnetic KIT-6 nano-composite and its amino derivatives by bearing acid-resistant iron oxide. The prepared materials exhibited excellent properties for U(VI) ions removal from aqueous solutions under various conditions. The experimental data show that the U(VI) adsorption features fast adsorption kinetics, high adsorption capacity and ideal selectivity toward U(VI). The adsorption process is of spontaneous and endothermic nature and ionic strength independence, and the adsorbents can be easily regenerated by acid treatment. Compared to pristine KIT-6, the introduction of magnetism does not reduce the efficiency of the material to remove U(VI) while exerting its role as a recovery adsorbent. The findings of this work further demonstrate the potential broad application prospects of magnetic hybrid mesoporous silica in radionuclide chelation.