[Objective] The differences of agricultural water use efficiency and its influencing factors between the Yellow River basin and the Yangtze River Economic Belt were studied in order to provide a scientific basis and reference for decision-making to effectively improve agricultural water use efficiency and sustainable agricultural development in the two regions.[Methods] Based on data from 19 provinces and cities in the Yellow River basin and the Yangtze River Economic Belt from 2009 to 2019, differences in agricultural water use efficiency and its influencing factors were analyzed by use of the super-efficiency SBM model, the Malmquist index, kernel density estimation, standard deviation ellipse, Tobit regression and other methods.[Results] ① Agricultural water use efficiency increased over time. The annual efficiency value for the Yellow River basin fluctuated greatly and internal differences were obvious. The efficiency center oscillated at the border between Shanxi Province and Shaanxi Province. However, the annual efficiency value for the Yangtze River Economic Belt fluctuated slowly, and its efficiency center moved to the southwest over time, and the annual average efficiency value was slightly higher than the efficiency value observed for the Yellow River basin. ② Technological progress was the main reason for the change in agricultural water use efficiency. The technological progress index for the Yellow River basin was slightly higher than the index of the Yangtze River Economic Belt from 2009 to 2019. ③ There was a great difference in the factors influencing the increase in agricultural water use efficiency over time between the two regions, and the reasons for the difference are closely related to the natural geographical environment and economic development.[Conclusion] Agricultural water use efficiency in the Yellow River basin and the Yangtze River Economic belt is generally good, but there are great regional differences. Therefore, targeted measures should be taken according to local conditions, and the efficiency of agricultural water use in the two regions should be promoted and continuously optimized from the perspectives of scientific and technological input, government guidance, and farmers' participation so as to produce sustainable development of river basin agriculture.