Considering the undesirable output, this paper adopted the data envelopment analysis (DEA) model with the slack variable and super efficiency improvement, to measure industrial water utilization efficiency in the Yangtze River Economic Belt. The paper also creatively introduces urbanization level and urban primacy into driver factors’ estimation by stochastic and fixed Tobit models, exploring how urbanization characteristics affected the water utilization in regional industrial production. The results showed that industrial water efficiency has maintained an upward trend during the whole period, while most central and western provinces have shown a U-shaped trend of decreasing first and then rising. However, the industrial water utilization efficiency of central regions is the lowest, and the eastern regions are the highest, catching up with western regions. Utilization efficiency shows an overall convergence during the research period from 2005 to 2017. Regarding the factors’ estimation, both population urbanization and land urbanization negatively affected industrial water utilization efficiency, particularly blind expansion and disorderly development. The urban primacy meant the unbalance of urbanization, which would lead to urban diseases and pollution transfer, while the effects of urban primacy depended on the urbanization level. However, the utilization efficiency of industrial water did not become better automatically along with urbanization development; therefore, the scale and speed of urbanization should be scientifically formulated. The effects of the level of economic development, the advanced industrial structure, and the level of foreign investment are significantly negative.