Mega-cities face complex and diverse endogenous development pressures and human-induced risks, and are also more vulnerable to the impacts and threats of natural disasters and climate change. Ecological restoration in mega-cities needs to focus on enhancing urban ecological resilience to cope with pressures and impacts from both internal and external systems, and to ensure the sustainable development of urban society and economy. Ecological restoration in mega-cities needs to focus on how engineering practices can enhance the resilience of urban ecosystems. Ecological resilience is one of the essential cores of urban sustainability. Urban sustainability demands that the urban complex ecosystem possesses the capacity to cope with and resist natural disasters and anthropogenic damages, the ability to recover from and adapt to stress and disturbances, as well as the capability to anticipate and prevent risks. The urbanization process and human activities have led to the encroachment and frequent disturbance of natural ecological spaces, resulting in highly fragmented and limited space for ecological restoration. Therefore, accurately identifying potential ecological restoration areas and setting clear restoration goals is of great significance. This study establishes a three-dimensional urban ecological resilience assessment system based on ecological networks and ecological security patterns, focusing on "ecosystem resistance, ecological source restoration, and ecological corridor adaptability," and conducts spatial identification for ecological restoration. Taking Beijing as a case study, the results show: ①Beijing has 51 ecological sources, accounting for 21.88% of its non-construction space, and 206 ecological corridors, mainly distributed in ecological conservation areas, providing ecological barriers and key ecological products for Beijing. ②The ecosystem resistance index is relatively low, with the northern deep mountains, Ling Mountain-Baihua Mountain, and eastern peripheral mountainous areas performing better. Ecological source restoration is good, while the adaptability of ecological corridors is generally low, requiring urgent restoration of ecological corridor functions. ③A total of 7277.07 km² of ecological restoration space has been identified, accounting for 55.21% of Beijing's non-construction space. This study provides a method for identifying protected restoration spaces based on ecological resilience, offering scientific guidance for ecological restoration planning in Beijing and providing a reference for ecological restoration planning in other mega-cities, aiming for a balance between conservation and development. By establishing the connection between the quantification of ecosystem resilience and the identification of regional ecological restoration spaces, and identifying ecological restoration spaces based on the level of ecosystem resilience, it can to a certain extent propose relatively effective strategies for the optimization and path of regional ecological restoration.