In the in-situ leaching method of ionic rare earth, ion exchange reaction between rare earth ions and leaching agent ions is carried out, which allows the rare earth ions to be leached from the ore body as the leaching solution flows through the pores. This indicates that the leaching process of rare earth ions is closely related to the seepage field, ion exchange field, and ion migration process of the leaching solution. In this study, an ionic rare earth mine located in Longnan of Jiangxi Province was taken as the research object. By conducting nuclear magnetic resonance scanning on the ore samples of this mine and vectorizing the nuclear magnetic resonance images, a two-dimensional geometric model of pores was obtained. Then, COMSOL Multiphysics software was used to establish a coupled numerical model of seepage–exchange–migration of the ionic rare earth mine during the leaching process at the pore scale to study the seepage situation of leaching solution with different injection strengths and concentrations, as well as the exchange and migration process. The results show that increasing the concentration of magnesium ions can increase the difference of ion diffusion concentration, accelerate the forward exchange rate of ions, promote the forward exchange reaction, and improve the concentration gradient of rare earth ions in the leaching solution. The more significant the diffusion effect, the higher the ion migration rate, while at the same time inhibiting the reverse adsorption of rare earth ions, and accelerating the leaching efficiency of rare earth ions. In addition, increasing the strength of the injection solution allows rare earth ions to leach out of the ore body earlier, shortens the leaching cycle, and thus reduces the peak concentration of leached rare earth ions. By analyzing the effects of the strength of the injection solution and leaching concentration on ionic rare earth leaching, the influence of those two factors on engineering economy can be briefly evaluated, which can be provided as a reference for the optimization of ionic rare earth mining technology.