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The acceleration of urbanization has brought significant changes to the urban underlying surface. As a result, the flood disaster caused by stormwater runoff has become increasingly prominent. The infiltration function of the permeable area can lead to flood disasters, but the extent and depth of the effect are still unclear. Therefore, based on the storm water management model (SWMM) and Green-Ampt infiltration model, this paper discussed the effect of improving soil saturated hydraulic conductivity (SSHC) and soil capillary suction head (SCSH) on the stormwater runoff process. The results show that the increase in SSHC and SCSH can significantly reduce runoff and increase infiltration. However, the improvement of SSHC can more effectively alleviate flood disasters compared with the improvement of SCSH. The change of SSHC has a significant effect on the stormwater runoff with a critical SSHC value while the effect can be ignored. In addition, there is a cross value; when the value of SSHC and SCSH is larger than the cross value, the difference between SSHC and SCSH in reducing runoff duration no longer exists. The critical value and cross value are not constant but change with the change of rainfall intensity. HIGHLIGHTS The effect of an urban underlying surface change on stormwater runoff is notionally studied.; Improving SSHC can reduce total runoff and increase total infiltration more effectively than improving SCSH.; There is an effect of rainfall intensity and urban IR in SSHC and SCSH on soil infiltration.; There exists a critical SSHC value, below which the change of SSHC has a significant effect on the stormwater runoff.;