With the increasing consumer awareness and knowledge about safe and healthy food, it is imperative to develop ‘green’ crops with reduced fertilizer application for quality food production, environmental protection and sustainable agricultural development. This study systematically evaluated and compared the water footprint (WF) including WFblue, WFgreen and WFgrey of eight crops including wheat, maize, rice, sweet potato, soybean, millet, mung bean and sorghum under green and traditional cultivation in the Huang-Huai-Hai farming region. The data came from 252 onsite questionnaires conducted in 2018 for land under green and traditional cultivation by 19 green planting companies and farming cooperatives with green food production certification authorized by the government of China. The results revealed that, compared to traditional cultivation, green cultivation under reduced N fertilizer application (1) decreased crop yields by 3–13%; (2) reduced the average WFtotal by 29% to 1168 m3 t−1 and average WFgrey by 57% to 419 m3 t−1 with no significant differences in WFblue and WFgreen; (3) decreased the WFtotal of maize by 55%, rice by 41%, wheat by 27%, mung bean by 31%, sorghum by 24%, sweet potato by 19%, millet by 17% and soybean by 17%. The WFgrey proportion of WFtotal under green cultivation ranged from 27–57% and contributed the most to the decline in WFtotal. This study offers insight into the impact of green cultivation on water requirements and pollution relative to traditional cultivation. Precision N fertilizer application and improved N use efficiencies on-farm are important pathways to sustainable agricultural development.