The grain yields of crops in the Zhuozhang River basin have an important relationship with irrigation due to a mismatch between precipitation and water requirements. In order to obtain optimal irrigation regimes of winter wheat and summer maize in different typical years (wet year, normal year, and dry year), a SWAT model (soil and water assessment tool) was set up in the study area and to simulate different irrigation treatments. According to calibration and validation results of runoff, evapotranspiration and yield simulation, the model showed high applicabilities in the main stream of the Zhuozhang. Different irrigation regimes showed a significant influence on yield, evapotranspiration (ET), water productivity (WP), and even runoff at the outlet. For both winter wheat and summer maize in each typical year, the peak value of crop yield did not meet the maximum value of water productivity. For winter wheat, treatments of W2, W3, and W6 (adopted in wet, normal, and dry years) can guarantee harvest effectively with the average runoff increased by 43.98%, 25.75%, and 6.38%, respectively, compared with actual irrigation. The average runoff increased by 1.58%, 2.89%, and 4.06%, respectively, with treatments of C8, C7, and C3 adopted in three typical years during summer maize growing periods.