The rapid economic development in the Chengdu–Chongqing Economic Circle (CCEC) has exerted significant pressure on the ecological environment of the Sichuan–Chongqing Region in China. Balancing ecological protection and economic development has become an imperative challenge that needs to be addressed. In this study, we employed land use/cover data and environmental threat factors to construct Ecological Security Patterns (ESPs) for the CCEC using the InVEST model and Circuit Theory. The research findings revealed the following key outcomes: (1) The total area of suitable habitat in the CCEC was 208,728.3 km2, accounting for 87.14% of the study area. Habitat quality exhibited regional variations, with higher quality habitats predominantly found in the western and northeastern parts, and lower quality habitats in the central region. (2) The CCEC consisted of areas with low, medium, high, and optimal habitat quality, spanning 140,912.18 km2, 15,341.89 km2, 15,578.38 km2, and 36,895.85 km2, respectively. These areas accounted for 58.83%, 6.40%, 6.50%, and 15.40% of the study area, respectively. (3) The ESPs in the CCEC encompassed 22 ecological nodes, 36 clusters of ecological corridors, and 136 ecological sources. Ecological corridors served as radial connections, linking each ecological node and ecological source along mountain ranges, forested areas, river networks, and valleys. (4) The core ecological regions forming the ESPs of the CCEC included the Qionglai–Minshan–Longquan Mountains in the west, Tiefeng–Fangdou–Qiyue–Wushan Mountains in the east and northeast, and Dalou Mountain in the southeast. These regional-scale findings provide valuable insights for policymakers to implement targeted measures for ecological protection and promote green development. They offer objective guidance and constraints for managing urban expansion and anthropogenic activities, ultimately enhancing the ecological security level of the CCEC.