A comprehensive indicator of water use efficiency (WUE) to promote coordinated development between socio-economic and environmental systems was developed. A comprehensive consideration of the social, economic and environmental benefits of water was made in the evaluation index system of WUE and the projection pursuit model combined with chaotic particle swarm optimization was adopted to calculate the comprehensive indicator of WUE. The Huai River Basin (HRB) was selected as a case study area. The temporal change of WUE showed that the annual WUE of the HRB from 2007 to 2013 increased obviously because of the enhanced emphasis on environmental protection by the government. The spatial results showed that the spatial WUE of each province in 2013 was significantly higher than in 2007. In 2013, Anhui with the lowest WUE was selected as representative to reveal the problems of water use in the HRB. The main reasons were that the government paid more attention to the high water consumption industries and ignored the small-scale water users, and wastewater treatment was still weak in the HRB. The research can provide the foundation for improving WUE and solving the problem of water shortages.

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