Trehalose, a nonreducing disaccharide, has been extensively applied to food, cosmetics, and pharmaceutical goods. The resultant solution of trehalose prepared by enzymatic methods includes high amounts of maltose. However, it is quite difficult to separate maltose and trehalose on an industrial scale because of their similar properties. In this paper, a high-performance resin was selected as a stationary phase to separate trehalose and maltose, and the resolution of these sugars was 0.59. The potential of a cation exchange resin was investigated as the stationary phase in separating trehalose and maltose using deionized water as the mobile phase. Based on the equilibrium dispersive model, the axial dispersion coefficients and overall mass transfer coefficients of maltose and trehalose were determined by moment analysis at two different temperatures, 50 and 70°C. Other parameters, including the column void and the adsorption isotherms, were also determined and applied to simulate the elution curves of trehalose and maltose. The simulated results matched the experimental data, validating the parameters. The optimized parameters are critical to the chromatographic separation of trehalose and maltose on an industrial scale.