Karst aquifers are known for their heterogeneity and irregular complex flow patters which make them more difficult to model. Although different modeling approaches have been used to make it through, they all have somewhat deficiency. This paper presents one such ap - proach which is based on MIKE-SHE. The model was applied in a Karst area of the Bajiang River Basin with support of the observed and GIS/ RS data. Modeling of evapotranspiration and flow in the upper part of the unsaturated zone is more detailed. The model was calibrated and validated by the observed discharge which was got from the Huangjianghzuang Station. The results show that the model is able to adequately simu - late temporal evolution of the river discharge, measured by Nash-Sutcliffe coefficient (0.84) as well as overall water balance. Besides, through the sensitivity analysis, we got to know that the precipitation was the key variable, and changes in spatial distribution of precipitation would cause the great influence on the results.