As an important agricultural product base in China, Henan province crosses the Qinling-Huaihe River demarcation line between the north and the south of China. The efficiency of water resources in Henan Province is of great importance for China to realize water saving, consumption reduction and green sustainable development. However, serious water pollution, environmental degradation and other problems restrict the local economy sustainable development. This study aims to analyze the ecological efficiency of water resources in Henan Province by using the super efficiency SBM and Malmquist index model. The results showed that: (1) the ecological efficiency of water resources in most cities fluctuated and increased during 2010-2019, while some regions showed a downward trend due to the influence of geographical location and climate, (2) the ecological efficiency of water resources varies greatly among cities from the perspective of the spatial pattern and the regions with higher ecological efficiency of water resources are concentrated in the economically developed centers which have a driving effect on the surrounding areas, (3) historical resources, economic development level and technological progress all have an impact on the eco-efficiency of water resources, among which technological progress has the greatest impact. In addition, suggestions on effective utilization of water resources are put forward according to its change rules and influencing factors.