Persimmon tannin modified chitosan (PT-CS) microspheres were synthesized by a water bath method using sodium tripolyphosphate (STPP) as a cross-linking agent for the removal of U(VI) from wastewater. The results showed that the optimal preparation conditions for PT-CS were a ratio of PT to CS mass of 4:1 and a reaction temperature of 80°C. When the initial concentration of U(VI) was 5 mg/L, and the pH value was 1.5, the PT-CS was injected at 0.06 g/L, and the reaction was 2.5 h. The removal rate of U(VI) from water reached 99.2%. The results of the deep removal test of U(VI) from rare earth wastewater showed that the concentrations of U(VI) in the combined wastewater and extraction wastewater were reduced from 4.42 mg/L and 2.12 mg/L to within 0.02 mg/L at pH 2.0, respectively. In contrast, the removal rate of high concentrations of Ca2+ in the wastewater reached 99%, meeting the emission standards of the rare earth industry.