Because of climate change and rapid urbanization, urban impervious underlying surfaces have expanded, causing Chinese cities to become strongly affected by flood disasters. Therefore, research on urban flood risks has greatly increased in the past decade, with studies focusing on reducing the risk of flood disaster. From 2012 to 2020, the impervious underlying surface has increased, and the permeable underlying surface has decreased annually in Kunming City. This study was conducted to investigate the impact of continuous changes in the urban underlying surface on flood disasters in the Runcheng area south of Kunming City from 2012 to 2020. We constructed a two-dimensional flood model to conduct flood simulations and flood risk analysis for this area. The relationship between the permeability of the underlying surface and urban flood risk was simulated and analyzed by varying the urban underlying surface permeability (30%, 35%, 40%, 45%, 50%, 55%, and 60%). The simulation results indicate that the urban flood risk increased with increases in the impervious underlying surface, with a threshold permeability of 35%. Once the permeability of the urban underlying surface decreased to below 35%, the flood risk increased rapidly. We demonstrated the impact of the urban underlying surface permeability on the risk of urban flood disasters, which is useful for urban planning decisions and urban flooding risk controls.