In this study, a method of simulating ephemeral stream runoff characteristics in Jeju watershed is newly suggested. The process based conceptual-physical scheme is established based on the SWAT-K and applied to Cheonmi-cheon watershed which shows the typical pattern of ephemeral stream runoff characteristics. For the proper simulation of this runoff, the intermediate flow and baseflow are controlled to make downward percolation should be dominant. The result showed that surface runoff simulated by using the modified scheme showed good agreement with observed runoff data. In addition, it was found that the estimated runoff directly affected the groundwater recharge rate. This conceptual model should be continuously progressed including rainfall interception, spatially estimated evapotranspiration and so forth for the reasonable simulation of the hydrologic characteristics in Jeju island.