When the permeability of landslide bed and landslide zone is very low relatively to the sliding mass, the influences of the runoff from upper slope would not be considered by existing methods in the numerical simulation of rainfall infiltration, so that the feed of precipitation infiltration is underestimated, hence the stability of landslide is overestimated. In this paper, based on Richards's equation, the kinematic wave equation and FEM, a 3D simplified numerical method considering the runoff under the rainfall condition is proposed. In the new method, the calculation domain only contains the sliding mass, to decrease the computational scale and to avoid computational difficulty caused by a significant difference of permeability between the landslide bed (and slide zone) and sliding mass. And what's more, the rainfall boundaries are corrected according to the terrain and net rainfall including not only fluxes but also types (head boundary and flux boundary). The new method is suitable for numerical simulation of the landslide infiltration when the permeability of the landslide bed and landslide zone is very low relatively to the sliding mass, and it can consider the influences of water supply from the runoff to the infiltration of the sliding mass. In order to show the necessity in considering the water supply and the validation of the new method, the infiltration process of a simple soil slope is simulated by the new method and an existing method. The comparisons are made in the aspects of water balance and slope seepage field. The simulated results show that the calculation results, the water balance and the effects of rainfall infiltration on the matric suction can be guaranteed when the runoff supplement is taken into account.