Quantifying the impact of global climate change on the water cycle and crop production is essential for water resource management and agricultural production planning. This study compared multiple GCM (General Circulation Model) projections of CMIP5 (Coupled Model Intercomparison Project 5) and CMIP6 and further used the selected GCMs to quantify the impact of future climate change on hydrology and crop production under intensive irrigation management in the North China Plain using an improved SWAT model (SWAT-MAD). Taylor’s skill score was used firstly to screen out six groups of GCMs with better simulation performance from 10 pairs of homologous GCMs of CMIP5 and CMIP6. The selected GCMs of CMIP5 and CMIP6 were further used to drive SWAT-MAD for a robust evaluation of climate change impacts. Results showed that during winter wheat growing season, average actual evapotranspiration (ET_a) increased by 3%, 3%, 4%, and 5%, respectively, under 2041–2070 RCP4.5, 2041–2070 SSP2-4.5, 2041–2100 RCP4.5, and 2071–2100 SSP2-4.5 scenarios, compared to the historical period (1971–2000). During summer maize growing season, those changes in ET_a were 4%, 2%, −0.2%, and −3%. Predicted future precipitation, air temperatures, and surface runoff could increase, while irrigation could decrease as precipitation increased. The dynamic patterns of leaf area index of winter wheat and summer maize indicated that there is a tendency for early emergence and maturity of both crops in the future, and the daily total biomass elevated with a corresponding increase in final yields. The highest increases in yields of winter wheat and summer maize were 18.9% and 16.7%. The findings not only contribute to enhancing the confidence of future projections using CMIP6 but also facilitate our understanding of the relative uncertainty of GCMs. This study provides technical and data support for pre-selections of GCMs and decision making in best management practices for groundwater conservation and agricultural production.