A new filter material, manganese oxide film coated clinoptilolite (MOFCC), was characterized and introduced to explore the effect in treating high concentration of manganese (1.71–2.12 mg L−1) from aqueous solution in fixed-bed column. Adsorption behavior of Mn(II) can be approximately described with the Langmuir isotherm. During the continuous 30 days filtration experiment, the removal rate of Mn(II) has maintained to be above 95.51%, the accumulated removal amount (806.42 mg) is much higher than the theoretical adsorption capacity (89.71 mg), which indicated that the removal of manganese by MOFCC includes both adsorption and auto-catalytic oxidation process, and it does not require a start-up period. SEM, EDS, XPS, XRD, ZETA potential and BET analyses were used to observe the surface properties of MOFCC. The manganese oxide film of MOFCC exhibits in clusters, apparently on occupied surface, the main component of the manganese oxide film is (Na0.7Ca0.3)Mn7O14·2.8H2O, the specific surface area of MOFCC is 38.76 m2 g−1, and the pore size is concentrated in the range of 3–40 nm, within the mesoporous range mesopores. pHpzc (point of zero charge) value is about 2.36. The characteristics of MOFCC make it an excellent manganese removal filter material for water treatment plant. Therefore, there is a long-term practical significance to develop new system for deep removal of manganese based on MOFCC.