Ion-adsorption-type rare-earth ores (IATREOs) that have experienced granite weathering have good permeability, and their leaching process involves the solute transport problem, which is dominated by convection. Because of the oscillation and dispersion errors of existing numerical methods for solving the convective-dominated solute transport equation, the results have low precision in the twin leaching process. In this paper, the convection–dispersion equation is decoupled into the dispersion equation, the convection equation, and the source-sink equation; the Crank–Nicolson and implicit difference methods are used to solve the dispersion equation and the source-sink equation, respectively. The solution of the convection equation is achieved on the basis of its physical interpretation. Therefore, a decoupling method for the convective-dominated solute transport equation is established. In comparison to the two examples with analytical solutions, the calculation errors of the method established in this paper are less than 2.00%, and it can solve the oscillation and dispersion problems. The rationality of the method is further demonstrated through the column leaching experiment of IATREOs. In comparison to the test results, the coefficients of determination of the breakthrough curves of rare-earth ions and ammonium ions calculated by the proposed method are all greater than 0.850, and the peak concentration error of rare-earth ions is less than 7.00%. This indicates that the proposed method can simulate the leaching process well. Furthermore, by combining the multiple/half method and the dichotomy method, an optimization method for determining the leaching agent amount was established to analyze the relationship between the leaching agent and the ratio of dispersion to pillar length. The results can provide a solution that can be used to mine IATREOs from experience to theory.