With 11 provinces in the Yangtze River Basin used as the research objects, an SEDEA window model for dynamic evaluation of water resources utilization efficiency in the Yangtze River Basin was established. In combination with the GIS spatial analysis method, spatio-temporal changes of the water resources utilization efficiency in the Yangtze River Basin were explored. The Malmquist index and Ward's clustering method were used to investigate factors that affect the water resources utilization efficiency. The results show that the water resources utilization efficiency of 11 provinces in the Yangtze River Basin had an overall upward trend from 2013 to 2019, and the water resources utilization level had significant spatial differences, with a distribution trend being strong in the east and weak in the west. The evolution trend of the Malmquist index of water resources in 11 provinces is basically the same as that of the technological progress index, indicating that the improvement of the Malmquist index is mainly due to the growth of the technological progress index, and the comprehensive technical efficiency index is an important factor restricting the improvement of the water resource utilization efficiency. Increasing scientific and technological investment and technological innovation, optimizing industrial structure, and rationally allocation of production resources are important ways to improve the water resources utilization efficiency.