In order to accurately evaluate the dynamic changes and distribution in water consumption quantity and efficiency of crop production at different spatial and temporal scales in a region, the AquaCrop model was applied at 5′ spatial resolution to estimate the blue and green water footprints (WFs) of wheat production in three typical hydrological typical years in Yellow River Basin (YRB). Irrigated and rainfed wheat were identified. Results showed that the annual average total WF and perunitproduct WF of wheat in YRB were 2.19×1010m3 and 1.22m3/kg, respectively. Blue WF accounted for 65% of the perunitproduct WF of wheat. The wheat WF was decreased from the upper reach to the lower reach in YRB. Traditional surface irrigation dominated the total blue WF and total green WF of wheat by occupying 92% and 50% of basin’s total amount, respectively. The WF under irrigated condition was 1.40m3/kg, which was higher than that under rainfed condition of 1.12m3/kg. The WF of wheat production in YRB was affected by irrigation methods. The basin average WF under micro irrigation was only 1.67m3/kg, while that of sprinkler irrigation was up to 2.07m3/kg. The result indicated that the effects of different water supply and irrigation methods on large-scale WF accounting can not be ignored. The quantification and evaluation of crop WF distinguishing different water supply and irrigation methods could be an important foundation for efficient utilization of agricultural water resources. The results can provide reference for WF accounting and regional agricultural water saving strategy formulated for different temporal and spatial scales.