Construction of ecological security pattern is a necessary means to ensure urban ecological security. Accurate identification of ecological sources is the basis for the construction of ecological security pattern. In this study, ecological source identification system is constructed in Shanghai, a highly urbanized metropolitan area. The influences of different land use data sources and index weights on the identification of ecological sources are investigated. On the basis of this identification, ecological resistance surfaces are constructed with the minimum cumulative resistance model (MCR) and circuit theory to identify priority areas for ecological protection and restoration, which could complement the existing studies that focus only on protection/restoration. The results show that (1) the naturally ecological background is still an important indicator for identifying ecological source areas, and the addition of human demand indicators can fill the lack of relevance and richness of existing studies for identifying highly urbanized source areas. The best recognition is reached when the weighting of ecosystem service pattern, ecological and environmental safety pattern and environmentally friendly pattern is 5:2:1. (2) The spatial and quantitative distribution of ecological sources in Shanghai is extremely uneven, and fragmentation is the primary problem. There were 202 ecological source sites in Shanghai in 2017, totaling 920.96 km², accounting for 14.53% of the total area, of which the number of micro-source (area <3 km²) was 82.67%. The level of urbanization affects the distribution of ecological sources. The outer ring is the watershed between the number of source sites and the total area, and the suburban ring is the important boundary of the average area of source sites. (3) Shanghai's ecological protection network is composed of surface (source sites)-line (corridors)-point (priority points), including 442 ecological corridors and 306 priority points for ecological protection, with important points and lines concentrated in the central urban boundary. The priority areas for ecological restoration in Shanghai are 325.47 km², including 309.78 km² of obstacle points, and 95 non-ecological patches (15.69 km²) need to be optimized. The priority areas for ecological restoration in the metropolitan area should focus on the areas of resistance to urbanization spreading, and more attention should be paid to grassland and arable land with moderate ecological value. The study can be used as a reference for identifying key areas for ecological restoration in other highly urbanized areas and cities in the process of rapid urbanization.