Water resource utilization efficiency is important for implementing the strictest water resource management system, constructing water ecological civilization,and promoting urban economic and social development in China. Through the categorical data enveloping analysis model and variation coefficient method, urban water use efficiency was measured in ecological geographic areas of China from 2007 to 2016. Additionally, influencing factors of water utilization efficiency was analyzed by Tobit model. It was found that the utilization efficiency of urban water resources was generally low in China, showing a fluctuation pattern of first declining and then rising, and the gap of water use efficiency among cities was narrowing. For the ecological geographic regions, efficiency of water resource utilization was significantly discrepant among different regions, decreasing successively from the temperate arid region, the temperate semi-arid region, the temperate sub-humid region, and the temperate humid region to the subtropical humid region. However, the difference in water resource efficiency of ecological geographic regions was shrinking gradually. In terms of influencing factors, the conclusion showed that the municipal population, land use structure, economic development level and industrial structure were positively correlated with water resource use efficiency, while urban water supply, water consumption structure and water management policy had negative effects.