To explore the evolution of characteristics of pore structure of a weathered crust elution-deposited rare earth orebody during the leaching process with different valence cations, leaching solutions with NH4+, Mg2+, Al3+ as cations were prepared to carry out simulated column leaching experiments. Nuclear magnetic resonance (NMR), scanning electron microscope (SEM) and energy dispersive spectrometry (EDS) were used to measure the microscopic characteristics of samples, then the and mechanisms of pore structure evolution of samples during leaching with different valence cations were analyzed. The results showed that: in the main reaction stage, ion displacement reaction in three different leaching solutions resulted in the top-down migration of solid fine particles; then the continuous evolution of secondary pore structure occurred, and then the drainage characteristics of leaching solution were affected. The evolution of pore structure of rare earth orebody induced by leaching solution with different valence cations was generally similar: the pore structure of the orebody firstly evolved from large pores to small pores; whereas at the end of ion exchange, the pore structure evolved from small pores to larger pores. However, there were significant differences in the pore proportion of different sizes. The number of large pores and extra-large pores in the samples of the ammonium sulfate leaching group was the largest, followed by the magnesium sulfate leaching group, and the least were found in the aluminum sulfate leaching group. The mechanism study showed that this difference was caused by the dynamic transformation (deposition and release) of fine particles of rare earth ore on the pore surface, which was affected by the change of ionic strength, the valence cation and the pH value of leaching solution caused by ion substitution.