Many countries have planned or implemented long-distance inter-basin water transfer projects to resolve water scarcity due to spatially imbalanced water application. The South-North water transfer project (SNWTP) in China is among the largest inter-basin water transfer projects built so far, which would transfer water from Changjiang (Yangtze) river to northern regions, in order to fulfill the gap between limited water supply and increasing water demand from civil, industrial, agricultural and ecosystem purposes. In order to research how will SNWTP influence future crop production, cropland expansion and irrigation water use, we use a model with global to spatial scale to project agricultural production from 2017 to 2050 with different SNWTP implementation and operation scenarios. Under current scenario of water transfer capacity, crop production would increase by 60.05% and cropland would expand by 4.01%. Increasing amount of water transfer from current level to full capacity of the whole SNWTP would decrease irrigation water use in water donating basins by 0.20% - 0.35%, while it would increase irrigation water use in water receiving basins by 0.4% - 4.67%. Along transfer routes, the mainstream Huai river basin is most responsive to SNWTP in irrigation water use, crop production and irrigated cropland expansion, where results indicate that impact of SNWTP would be spatial heterogeneous on local level as well. The multi-scale analysis of SNWTP’s agricultural impact implies the importance of taken local impact and response of inter-basin water transfer into planning and associated policy making.