A robust identification system of territory space ecological restoration and conservation can make effective contribution to regional ecosystem restoration and conservation. However, current research and planning lack the identification of key ecological restoration and conservation areas from the perspective of systematicness and integrity. This study established a systematic spatial identification method for ecological restoration and conservation to provide basis for regional coordinated development and regional ecological security. On the basis of the method, taking Beijing as a case, the spatial pattern of ecosystem restoration and conservation was explored through assessing of ecosystem services, ecosystem quality and ecological problems. The results showed that:(1) the ecosystem quality and ecosystem services increased generally in Beijing from 2000 to 2015. Ecosystem quality of forest, shrub and grassland improved by 39%. Correspondingly, water retention service, soil conservation service and flood mitigation service increased by 11%, 3% and 10%, respectively. However, ecological degradation occurred in some regions because of nature or human activities impact. The degraded areas of ecosystem services and ecosystem quality from 2000 to 2015 were mainly concentrated in the plain and the north of Miyun Reservoir, covering a total area of 760.4 km² dominated by farmland and urban land. The areas with low ecosystem quality were mainly distributed in the mountainous areas of southwest and northeast, covering an area of about 4925 km² dominated by forest and shrub ecosystems. The areas with severe soil erosion were scattered in mountainous areas, covering an area of about 130.1 km² dominated by farmland and shrub. The suggested ecological restoration regions in Beijing consisted of the above mentioned three, with a total area of about 5606 km²., accounting for 34.16% of the total area of Beijing. (2) The area of ecological conservation suggested was 6391 km², accounting for 38.95% of the total area of Beijing, mainly distributed in the northern and southwestern mountainous areas. The forest, shrub, grassland and wetland accounted for 54.81%, 34.38%, 6.53% and 4.27% of the total area of the ecological conservation space, respectively. The ecological conservation areas of Beijing could conserve 79.63% of Beijing's water retention service, 74.97% of soil conservation, 58.79% of flood regulation and storage, and 60.3% of Beijing's natural habitat. The spatial identification system of ecological restoration and conservation constructed in this study could not only serve as scientific basis for ecological restoration and conservation planning and ecological security pattern construction in Beijing, but also provide references for ecological restoration and conservation in other areas.