The improvement of water resource utilization efficiency is helpful to the green transformation of industry and the construction of a water-saving society. Based on the SBM method, this paper estimated the green total factor productivity of water resources in Anhui Province from 2010 to 2018 and used the Malmquist index decomposition model to study the regional distribution characteristics of green total factor productivity of water resources and the dynamic change of the decomposition index. The results show that the overall water resource use efficiency in Anhui province is relatively high, with regional characteristics of “Central Anhui > Southern Anhui ≈ Northern Anhui”. The water resources use efficiency in Central Anhui Province fluctuates greatly in the early stages, but tends to be stable in recent years. The difference in water resource use efficiency in Anhui Province in different regions is decreasing and tends to be consistent. The cities with low water resource use efficiency have an obvious “late-development advantage”, and the convergence rate of each region presents the characteristics of “Southern Anhui > Central Anhui > Northern Anhui”.