Unsaturated layered soils are common in nature and engineering practices, including highway embankments and waste landfills. Based on the principle of effective stresses and considering the deformation in unsaturated porous medium and changes in permeability with the stress state during rainfall, a one-dimensional model for simulating coupled seepage and deformation in layered unsaturated porous medium is established. A finite element program was written in FlexPDE to analyze the hydro-mechanical coupled process of rainfall infiltration into a two-layer unsaturated porous medium. The factor of safety as a function of the wetting front depth is discussed based on a simple infinite slope analysis. The numerical results demonstrate that the coupling of seepage and deformation plays a significant role in the movement of wetting front, the distribution of pore-water pressure, and the slope stability. The coupling of seepage and deformation should be taken into account when analyzing the rainfall infiltration into the layered unsaturated porous medium, especially for a combination of a short-duration heavy rain and high initial suctions.