Water and energy are not only the foundation of high‐quality development in rural areas but also important constraints. Exploring the inner relationship between water, energy, and economic development has important significance for the high‐quality development in rural areas. This paper first constructs the evaluation index system of high‐quality development in rural areas, and quantifies high‐quality development levels in rural China from 1997 to 2021. Second, from the perspective of water footprint, the Super‐slack based measure model is used to calculate sustainable development efficiency under the constraint of water and energy. Finally, kernel density function, Gini coefficient method, and Tobit model are used to explore the evolution trend, regional differences, and driving factors of sustainable development efficiency in rural China. The results show that: (1) Under the constraint of water and energy, sustainable development efficiency in rural China is relatively low, showing a fluctuating trend of first rising and then declining. The efficiency in the western and eastern regions is higher than the national average, while the central region is the lowest. (2) The evolution trend of sustainable development efficiency in rural China, both the eastern and the western regions, shows the characteristics of “decreasing efficiency and weak polarization phenomenon,” while the central region shows the characteristics of “decreasing efficiency and no polarization phenomenon.” (3) The regional differences illustrate a fluctuating upward trend, which is mainly caused by the hypervariable density, followed by the differences among provinces in the eastern region. (4) Economic development, opening up, and rural marketization are the main factors.