To prevent the degradation and destruction of ecosystems, ecological restoration has become a worldwide issue. In recent years, China has been comprehensively carrying out relevant work on national spatial ecological restoration planning, among which the work on ecological restoration zoning can provide strong support for the implementation of ecological restoration strategies. We propose a theoretical framework and technical route for ecological restoration zoning from the hydro-ecological perspective, and suggest forming a regional ecological restoration zoning system based on the watershed as the basic unit and the dynamic evolution process of hydro-ecology as the core. We conduct an empirical study in Yanqing District, Beijing. The results show that: (i) From 2000 to 2022, the hydro-ecological comprehensive index of Yanqing District shows an upward trend. In terms of spatial pattern changes, it roughly shows a rising trend in the northeastern and southern mountainous areas, and a downward trend in the central-western and southwestern basins. (ii) Six types of ecological restoration zones are formed with the watershed as the basic unit. Zone Ⅰ accounts for the largest area (26.87%), and Zone Ⅵ accounts for the smallest proportion (7.14%). (iii) The proportion of areas with good or superior hydro-ecology in the Ecological Policy Zone of Yanqing District increased by 15.89% from 2000 to 2022, which is significantly higher than the average level, confirming the effectiveness of ecological policies such as nature reserves. This study provides a paradigm for ecological restoration zoning from the hydro-ecological perspective, and provides assistance for regional ecological restoration and sustainable development in China and even globally.