This study aims to improve the flood simulation accuracy in karst areas. Based on the concepts of freewater reservoir and linear reservoir, a distributed rainfall-runoff simulation method was proposed to consider the regulation effect of epikarst and deep subsurface fracture on water storage. A grid-based karst distributed hydrological model(GKDHM)was established by introducing the water storage modules of epikarst and deep subsurface fracture into the grid-Xinanjiang(GXAJ)model. The GKDHM was further tested through its application to a typical karst-dominated watershed, the Puting River Watershed. The results show that the simulation accuracy of the GKDHM in the Puting River Watershed is apparently higher than that of the GXAJ model, and compared to the GXAJ model, the GKDHM decreased the average relative runoff error of 20 flood events by 4. 92%, decreased the average relative flood peak error by 3. 59%, and increased the average deterministic coefficient by 0. 23. With the GKDHM, the water storage regulation effects of epikarst and deep subsurface fracture can be accurately simulated using distributed freewater reservoirs of epikarst and linear reservoirs of deep subsurface fractures when detailed information of the spatial distribution of karst-dominated area is available. The GKDHM is also capable of well considering the rocky desertification of the watershed through rational determination of the spatial distribution of its parameters. The simulated runoff components by the GKDHM are apparently more reasonable than those by the GXAJ model. In conclusion, the developed GKDHM can effectively improve the accuracy of flood simulation in the Puting River Watershed.