Based on the entropy weighting method, a comprehensive assessment system for the relationship between scientific and technological innovation and water use efficiency was constructed. The indexes of innovation and water use efficiency were calculated for Anhui Province as an example. By use of SPSS19. 0, the marginal contribution of scientific and technological innovation to water use efficiency were calculated based on the canonical correlation analysis and partial least-squares regression analysis method. The path analysis method was adopted to investigate the direct and indirect effects of scientific and technological innovation on water use efficiency. The results show that the scientific and technological innovation index of Anhui Province jumped from 0.0129 in 2005 to 0.9742 in 2014, while the water use efficiency index rose from 0. 4616 in 2005 to 0.8558 in 2014, indicating a synthetic evolution. The total elasticity coefficient of scientific and technological innovation to the marginal effect of water use efficiency is 0.09799, among which, the direct elasticity coefficient is 0.065253 and the indirect elasticity coefficient is 0.032737. The indirect elasticity coefficients of economic growth, regulation policy and industrial structure are 0.02583, 0.00754 and 0.00027 respectively. Based on the research results, the policy suggestions are proposed to improve water use efficiency.