Urban ecosystems are under enormous pressure in the background of rapid urbanization. Mountainous cities are more prone to degradation due to dramatic topography. Ecological security patterns combined with circuit theory can effectively identify ecological barriers and "pinch points" and propose targeted ecological restoration and protection strategies. In order to ensure the ecosystem health and sustainable development of mountainous cities, this paper applies the MSPA model, Invest model, MCR model, and Linkage Mapper Tools to identify the ecological source regions, eco-corridors, and "key points" in the central metropolitan area of Chongqing. The study shows that: (1) There are 43 ecological sources in the central urban area of Chongqing, with a total area of 986.56 km2, and it forms a linear distribution with a multi-patch scattering pattern. (2) A series of 86 ecological corridors in the area, totaling 315.14 km, show a pattern of more corridors in the east and fewer in the west. (3) The research found 17 sites totaling 24.20 km of the ecological corridor in the barrier point zone. In addition, up to 22 segments, totaling 19.27 km of the ecological corridor, are located in the "pinch point" zone. (4) The barrier point and "pinch point" on the ecological corridors are identified to obtain their type, scale, and location, thus suggesting conservation-restoration.