Magnesium salts are commonly employed as ammonium-free leaching agents in the extraction of weathered crust elution-deposited rare earth ores (WCE-REO). Nonetheless, these salts frequently face technical challenges, including relatively low leaching rates and inadequate permeability in the in-situ leaching process. In this study, cetyltrimethylammonium chloride (CTAC) was used as a novel leaching aid agent to improve the rare earth leaching process. The effects of CTAC and pH on the rare earth leaching behavior and permeability was investigated. The leaching kinetic model was established and the regulation mechanism by which CTAC interacts with clay mineral surfaces was revealed for rare earth leaching process enhanced by CTAC. The results indicate that the appropriate amount of CTAC can increase the permeation velocity by 1.16×10−4 cm·s−1. Moreover, the rare earth leaching rate increased from 83.75 % to 95.65 %, accompanied by a reduction in leaching equilibrium time under optimal conditions. However, a higher concentration of CTAC results in a lower permeation velocity due to the increasing viscosity and the hydrophilicity. The relatively low pH will affect permeability of composite leaching agent in the ore pillar, diminishing its beneficial impact on rare earth leaching. The kinetic equation, fitted by the shrinking core model, suggests that the leaching adheres to an internal diffusion control mechanism, underscoring mass transfer as the pivotal limiting factor in rare earth leaching. CTAC reduces surface tension and viscosity, facilitating the permeation of the leaching solution into the rare earth ore. Furthermore, CTAC can be adsorbed on the surface of rare earth mineral particles, increasing the contact angle of clay minerals, elevating the Zeta potential, and diminishing the thickness of the diffusion layer, thus promoting mass transfer during leaching. The results of atomic force microscopy (AFM) analysis shows that the appropriate amount of CTAC adsorbed on rare earth ores can decreases the thickness of the hydration film on the particles’ surface, further improving the mass transfer efficiency during the leaching process. The findings of this study offer new insights into the green and efficient extraction of rare earth resources from both theoretical and technical perspectives.