To estimate water balance of Pyosun watershed in Jeju Island, a three-dimensional finite difference model MODFLOW was applied. Moreover, the accuracy of groundwater flow modeling was evaluated through the comparison of the recharge rate by flow modeling and the existing one from water balance model. The modeling result under the steady-state condition indicates that groundwater flow direction was from Mt. Halla to the South Sea and groundwater gradient was gradually lowered depending on the elevation. Annual recharge rate by the groundwater flow modeling in Pyosun watershed was calculated to 236 million m3/year and it was found to be very low as compared to the recharge rate 238 million m3/year by the existing water balance model. Therefore, groundwater flow modeling turned out to be useful to estimate the recharge rate in Pyosun watershed and it would be available to make groundwater management policy for watershed in the future.