Natural soil slopes often consist in two or more soil layers due to the geological and human factors. Under heavy rainfall, rainwater infiltrates into the slope, and when the rainfall intensity is greater than the infiltration rate of the soil, the runoff occurs very shortly on the slope surface. Understanding the interaction process of slope runoff and surface infiltration under rainfall conditions is critical for flash flood and landslide risk management. However, the mechanism of the interaction between surface and underground seepage of layered soil slopes has so far remained poorly understood. The study of rainfall infiltration into the two-layered slope with coarse-over-fine stratification usually ignores the influence of slope runoff, and leads to an infiltration analysis that is not realistic. A coupled model was established to analyze the rainfall runoff and the rainwater redistribution process after rainfall, and the corresponding calculation program was compiled by Python to solve this problem based on the Moore two-layer infiltration and slope runoff governing equations. The numerical analysis results show that the rainfall infiltration process of the slope soil is related to the runoff depth on the slope surface. When rainfall intensity is smaller than hydraulic conductivity of surface soil, initial infiltration rate is equal to rainfall intensity, and gradually decreases with the rainfall duration after the runoff on the slope, and finally tends to be stable. The infiltration rate dramatically drops and eventually equals the permeability of the subsoil when the wetting front crosses the interface of the soil layers. It indicates that the infiltration rate of the slope with coarse-over-fine stratification is mainly controlled by the lower fine soil layer. The runoff is rapidly degraded after the rainfall stops, and the infiltrated rainwater continues to move downward under the combined action of gravity and the matrix suction of the soil under the wetting front. The runoff is rapidly degraded after the rainfall stops, and the infiltrated rainwater continues to move downward under the combined action of gravity and the matrix suction of the soil under the wetting front. The depth of wetting front tends to be gentle with rainwater redistribution. The example shows that the calculation model and calculation method are feasible, which can better reflect the rainfall infiltration process of the actual layered soil slope, and provide calculation basis for similar layered soil slope.