Abstract: Rainfall is the main factor inducing landslide disasters in ionic rare earth mines, where the seepage mechanisms and landslide characteristics of layered slopes differ significantly from those of homogeneous slopes. In the context of in-situ ionic rare earth leaching engineering, a numerical simulation analysis was conducted to investigate the changes in pore water pressure and volumetric water content in various soil layers of the slope during heavy rainfall. The rainfall intensities were set at 10 mm/h and 20 mm/h. The safety stability coefficient of slopes with different soil orders was obtained by the finite element strength reduction method, and the influence of different soil orders on slope stability was analyzed. The results showed that rainfall intensity and duration significantly affected layered slopes’ hydraulic behavior and stability. Specifically under rainstorm conditions, saturated water retention zones were more likely to form at the soil interfaces inside the sand-silty clay layered slopes, leading to a sharp increase in pore water pressure, significantly reducing soil shear strength and increasing the landslide risks. In contrast, as for silty-sandy clay layered slopes, the low permeability of their upper silty clay layers restricted vertical water infiltration, forming perched water zones that induced softening effects and increased the risk of slope instability. Under heavy rain and storm conditions, the safety coefficient of the silty-sandy clay layered slopes was lower than that of sand-silty clay layered slopes. Due to the severe water retention in the sand-silty clay layered slopes, their safety coefficient change was more significant.