In Jeju island, the surface runoff characteristics are quite different from those of inland. Most of streams show dried characteristics by means of large portion of recharge which goes to the deep aquifer. For this reason, the accurate estimation of hydrologic components by using watershed model like SWAT is very difficult. On the other hand, the integrated SWAT-MODFLOW model is able to simulate the complex runoff structure including stream-aquifer interaction, spatial-temporal groundwater recharge and so on. The comprehensive results of Pyoseon region in Jeju island show that the amount of groundwater discharge to stream is very small, but it might be added to the discharge into the sea. Statistical analysis shows that SWAT-MODFLOW's results represent better than SWAT's. Also, SWAT-MODFLOW produces a reasonable water budget which shows a quite similar pattern of observed one. This result proves that the integrated SWAT-MODFLOW can be used as a proper tool for hydrologic analysis of entire Jeju island.