Water scarcity is a key factor for the stability and sustainability of agricultural productivity in Huang-Huai-Hai Plain. Considering water shortage may be aggravated by climate change, cropping structure should be adjusted to alleviate the worsening situation. Based on the multi-model datasets of three representative concentration pathways (RCP) emission scenarios from IPCC5, the effect of climate change on water balance at sub-basin scale during 2011-2059 was assessed by VIP (soil-Vegetation-atmosphere Interface Processes) model. For the sub-basins with most serious shortage of water resource, two groundwater balance scenarios were proposed based on the principle of groundwater exploitation and infiltration balance. One scenario (scenario A) supposes that there is no inter-basin water transfer in 2050s, the other (scenario B) supposes that the inter-basin water transfer remains the average level in 2000-2010 in 2050s. The balance between water supply and demand is kept stable by shrinking the planting area of crop with high water consumption in both scenarios. The effect of climate change on planting area and yield of winter wheat in the two scenarios was assessed by VIP model. The results showed that the rainfall surplus in the whole plain will decrease 0.1%-14.1% in 2050s from low emission scenario to high emission scenario since the crop evapotranspiration increases more quickly than the precipitation does. In the north part of the plain water deficit will be exacerbated, and in the south part of the plain rainfall surplus will decrease. With respect to water balance, the planting area of winter wheat in Huang-Huai-Hai Plain should be shrunk 9.8%-11.3% in scenario A and 7.0%-8.8% in scenario B in 2050s, however, the wheat yield will increase 0-11.9% and 3.0%-15.9% in corresponding scenario due to the CO_2 fertilization. Shrinking planting area of winter wheat can effectively mitigate the agricultural water shortage in Huang-Huai-Hai Plain. The research results can provide underpinnings for government's decisions.