The invention relates to a condensate polishing mixed bed cation-anion resin separation filter. The filter comprises a resin pot, a main water inlet tube, and a resin inlet tube, a first resin outlet tube, a second resin outlet tube and a third resin outlet tube which are sequentially connected with the vertical side of the resin pot from top to bottom, the main water inlet tube is branched into a top water inlet tube and a bottom water inlet tube, the top water inlet tube is connected with a backwashing water outlet tube, the top water inlet tube is connected with the vertical top of the resin pot, and the bottom water inlet tube is connected with the vertical bottom of the resin pot. The invention also relates to a control method of the filter. The method sequentially comprises the following steps: 1, introducing resins into the resin pot; 2, backwashing the introduced resins; 3, leading out anion resins; 4, leading out middle-layer resins; and 5, regenerating to lead out cation resins. In the invention, the cation resin separation rate is increased, the mixed bed running time is prolonged, the acid and alkali consumption amounts are reduced, and the wastewater discharge is reduced.