The product water footprint (WF) is defined as the direct and indirect consumption of water resources in the process of product production. The complete water consumption of agricultural products includes the direct water consumption of crops in the field and the indirect consumption of relevant inputs in the crop production supply-chain. However, previous studies on the WF of agricultural products only focused on the direct water consumption in the field. Here, within the framework of WF standard quantification and life cycle method, a quantitative framework for the supply-chain based water footprint (SWF) of agricultural products production that indicated both indirect and direct water consumption along the raw material-to-product chain at an intra-national level was proposed. Then, the SWFs of wheat and its processed products (wheat flour and wheat bran) in mainland Chinas provinces in 2016 was quantified. Results showed that the national average SWF of wheat production was 4869m3/t, and the indirect WF related to means of production accounted for 6% of the total SWF of wheat. The SWFs of wheat flour and wheat bran production were 3781m3/t and 11037m3/t, respectively. There was significant spatial heterogeneity in the intensity and composition of the SWF of wheat and derived products production, and the contribution of the indirect blue WF of Fujian wheat to the total blue WF reached 25%. The results can provide a scientific basis for comprehensively analyzing the internal relationship between agricultural and industrial water input among regions and for formulating reasonable water resources allocation scheme and implementing the stratagem of “deciding production by water”.