Improving the efficiency of water resources utilization in China's provinces and cities and eliminating the constraint effect of water resource utilization on economic growth to the greatest degree may promote the full implementation of the Belt and Road Initiative from the perspective of water resources. Based on super efficiency DEA model and Malmquist index, the paper measures the panel data from 2011 to 2015 of the Belt and Road Initiative's 18 provinces and municipalities in water utilization efficiency and then applies the Tobit model to test its influential factors. The result shows that the overall level of water utilization efficiency of 18 provinces and municipalities is good. There is a growth trend of water utilization efficiency and the differences between provinces and cities are large. The water utilization efficiency of whole regional shows the increasing tendency from eastsouth, northwest, northeast to westsouth. Technological progress is the influential and decisive factors which have impact on the change of water resources total factor production efficiency. GDP per capita and water production-supply enterprises' output value per capita have positively correlated relationship with water efficiency while water resource per capita, water conservancy and environment and public facilities investment per capita, industrial water, and agricultural water utilization, the number of production- supply enterprises have negative correlated relationship with water efficiency. Therefore, the paper proposes the following the ways to improve water efficiency: strengthening the inter-regional technical cooperation, optimizing the structure of agricultural water use, investing properly in water conservancy projects, and further promoting the construction of water rights market.