Water and energy are main inputs for the food production and supply, a lot of water is used for energy production and a huge amount of energy is used for water system. To study the water energy food linkage in economic system within China, we built the water energy food nexus accounting framework based on multiregional input output analysis. The water use for different energy and food types, energy consumption for all stages of water use and different kinds of food production for each region were inventoried. Then the direct and indirect energy and water embodied in monetary flows among regions were calculated via multiregional input output analysis to analyse embodied energy, water and their related flows. Then we identified the critical regions and flows in water energy food nexus system for nexus management. The primary results showed that megacities are the crucial regions for nexus management, among which Shanghai, Hainan and Tianjin are crucial regions for energy management with high hybrid embodied energy consumption, and Shanghai, Beijing, Tianjin and Zhejiang are crucial regions for water management with high hybrid embodied water consumption. The main export import pairs for hybrid embodied energy are Shandong Tianjin, Jiangsu Shanghai, Shandong Shanghai and Shandong Beijing, which should be critical pathways for nexus management. And main export import pairs for hybrid embodied water are Shandong Tianjin, Shandong Shanghai, Shandong Zhejiang, Henan Guangdong, Henan Zhejiang and Hebei Beijing. By identifying the critical nodes and flows in water energy food nexus system, this study aims to investigate regional interactions as for water, energy and food and provide a better way for regional water, energy and food coordinated management. (C) 2017 The Authors. Published by Elsevier Ltd.