Since 1999, large‐scale ecosystem restoration has been implemented in the Loess Plateau, effectively increasing regional vegetation coverage. Vegetation restoration has significantly elevated the saturated hydraulic conductivity (Ks) of the near‐surface soil layers and increased the vertical heterogeneity of the Ks profile. Many studies have examined the change of runoff due to revegetation, yet the impacts of Ks profile on the soil moisture distribution and runoff generation processes were less explored. In this study, numerical simulations were conducted to investigate how changes in the Ks profile caused by vegetation restoration influenced the hydrological responses at event scale. The numerical simulation results show that the increase of surface Ks caused by vegetation restoration can effectively reduce runoff at event scale. Moreover, the enhancement of vertical heterogeneity of Ks profiles can significantly change the vertical profile of soil water content, prompting more water to percolate into the deep soil layer. When rainfall exceeds a threshold, the accumulation of soil water above the relatively less permeable layer can cause short‐term saturation in shallow soil layers, resulting in a transient perched water table. As a result, after the vegetation restoration in the Loess Plateau, though Horton overland flow is still the main runoff generation mechanism, there is a possibility of the emergence of Dunne overland flow under the high vegetation coverage (e.g., NDVI larger than 0.5). This emergence of new runoff generation mechanism, saturation excess runoff, in the Loess Plateau due to the vegetation restoration could provide scientific guidance for water and sediment movement, soil and water conservation practices, and desertification control in the Loess Plateau.