Ionic rare earth ore is a type of featured rare earth ore in China. Its mining process suffers from a long leaching cycle and considerable consumption of leaching agents. Improving mining efficiency requires a sound physical understanding of the leaching process. In this study, the CFD-based numerical model is used to analyze the physical process of leaching through porous media formed by particles. The simulation results indicate that a lower packing porosity and smaller particles packed granular porous medium result in much larger energy dissipation during seepage, and the energy dissipation increases with seepage velocity. It is found that when the seepage velocity increases to a certain high value, the energy dissipation exceeds the value predicted by Darcy’s law, which is mainly caused by liquid turbulence. Additionally, the effect of particle shape is examined. The results show that the granular medium composed of prolate particles causes larger energy dissipation than oblate particles, and spherical particles play the least role. This phenomenon may result from the particle shape affecting the area of the frontal contact surface between particles and liquid. The results provide new insights into the fundamental understanding of percolation and seepage behaviors in the ion-adsorption-type rare earth ore leaching process.