We used numerical models to reliably analyze the groundwater flow and hydraulic conductivity on Jeju Island. To increase reliability, improvements were made to model application factors such as hydraulic watershed classification, groundwater recharge calculation by precipitation, hydraulic conduction calculation using the pilot point method, and expansion of the observed groundwater level. Analysis of groundwater flow showed that the model-calculated water level was similar to the observed value. However, the Seogwi and West Jeju watersheds showed large differences in groundwater level. These areas need to be analyzed by segmenting the distribution of the hydraulic conductivity. Analyzing the groundwater flow in a sub watershed showed that groundwater flow was similar to values from equipotential lines; therefore, the reliability of the analysis results could be improved. Estimation of hydraulic conductivity distribution according to the results of the groundwater flow simulation for all areas of Jeju Island showed hydraulic conductivity > 100 m/d in the coastal area and 1 45 m/d in the upstream area. Notably, hydraulic conductivity was 500 m/d or above in the lowlands of the eastern area, and it was relatively high in some northern and southern areas. Such characteristics were found to be related to distribution of the equipotential lines and type of groundwater occurrence.