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In this study, an ecological network-based input-output model (ENIOM) is developed for assessing the virtual water in China. Direct/indirect water consumption efficiency and virtual water flow directions among different sectors are quantified by input-out model, and the relationship (e.g., exploitation, competition and mutualism) among different sectors are identified by network utility analysis. Based on China’s input-output table in 2017, results show that (i) agriculture sector has the highest direct water consumption coefficient, and manufacturing sector has the highest indirect water consumption coefficient; (ii) manufacturing sector is the largest virtual water input and output sector, with a total net input of 93.6×109 m3 from the remaining seven sectors; and (iii) exploitation is the main relationship existed in the water network system. These findings suggest that more attentions should be paid on agricultural and manufacturing sectors in terms of water resources management.