China is a country of agriculture, and agricultural production consumes a great deal of water. In this paper, we quantify the provincial food production water footprint (WF) in China during 1997–2011, and then analyze its change trend by the method LMDI (Logarithmic Mean Divisia Index). The results indicate that: (1) China's food production WF increased during 1997–2011 as a whole. The food production WFs at the provincial level are obviously different. (2) The main reason for the change of WF of food production in China related to the virtual water content and total food production. As for the changes of food production WFs for each province, they were not always in accordance with the total food production. For example, in Guizhou, Qinghai, Sichuan, and other provinces, the food production WFs grew while total food production declined, thus indicating strong negative decoupling. Thus, it is necessary to take the measure of agricultural products' transportation ‘green channel’ to promote the development of domestic food trade and virtual water trade.