The likelihood of future global water shortages is increasing and further development of existing operational hydrologic models is needed to maintain sustainable development of the ecological environment and human health. In order to quantitatively describe the water balance factors and transformation relations, the objective of this article is to develop a distributed hydrologic model that is capable of simulating the surface water (SW) and groundwater (GW) in irrigation areas. The model can be used as a tool for evaluating the long-term effects of water resource management. By coupling the SWAT and MODFLOW models, a comprehensive hydrological model integrating SW and GW is constructed. The hydrologic response units for the SWAT model are exchanged with cells in the MODFLOW model. Taking the Heihe River Basin as the study area, 10 years of historical data are used to conduct an extensive sensitivity analysis on model parameters. The developed model is run for a 40-year prediction period. The application of the developed coupling model shows that since the construction of the Heihe reservoir, the average GW level in the study area has declined by 6.05 m. The model can accurately simulate and predict the dynamic changes in SW and GW in the downstream irrigation area of Heihe River Basin and provide a scientific basis for water management in an irrigation district.