Using the panel data of eleven provinces in Yangtze River economic zone from 2005 to 2014, the total-factor water resource use efficiency including undesirable goods is measured based on the input-oriented super-efficiency DEA-CCR model, and then, the water resource use efficiency is analyzed by using the Malmquist index. The main influencing factors for the increase and decrease of the total-factor water resource use efficiency are investigated, and the variation trend of the water use efficiency in various industrial regions is determined. The results show that the industrial water use efficiency in various provinces has large difference, and it is the highest in the downstream and the lowest in the middle reaches of Yangtze River economic zone. The water use efficiency of the whole economic zone has an increase trend from 2005 to 2014. The technical progress is the major power to promote the total-factor water resource use efficiency. The industrial water resource use efficiency of Yangtze River economic zone exhibits a convergent trend and, the gap among various provinces decreases.