Rainfall is one of the most critical factors that results in the landslide instability. However, the influence of runoff from bedrock slope on infiltration has not been considered by the existing numerical methods so that unfavorable infiltration is underestimated and the stability of landslide, especially those deep slides, is overestimated. In this paper, based on Richards’s equation and FEM, a 2D simplified numerical method is proposed, which can consider the influence of runoff supply on the infiltration of sliding mass. In the proposed method, calculation domain only contains sliding mass in order to avoid the numerical problems induced by the large difference between the permeability coefficients of landslide body and landslide bed (or slide zone), and rainfall boundaries are corrected according to the horizontal length of bedrock slope and saturation of slope surface. The seepage field and stability of an existing landslide in the Three Gorges Reservoir Area are simulated under the water level fluctuation of reservoir and the rainfall from Oct., 2006 to Dec., 2009. It is shown that the saturated zone in the trailing edge of landslide becomes significantly enlarged when the runoff supply is considered, and thus the stability decreases more significantly, which is consistent with the data from the displacement monitoring. In addition, rainfall trivially influences the stability of landslide if the runoff supply is not taken into account.