Urban biodiversity faces threats from habitat loss, landscape fragmentation, and human disturbances. Ecological networks (ENs) can enhance habitat connectivity and bolster population resilience to disruptions. To safeguard the biodiversity of Nanjing's urban area, this study selected understory insectivorous birds as indicator species for biodiversity, employing a comprehensive approach integrating the maximum entropy (MaxEnt) model and the area threshold method to delineate ecological source areas. Key indicators directly linked to the species distribution were extracted based on the habitat suitability assessment results, and an ecological resistance surface was crafted using spatial principal component analysis. Subsequently, the circuit theory model was applied to pinpoint ecological corridors, pinch points, and barrier points. The findings unveiled the following: (1) The normalized difference vegetation index (NDVI), human activities (HA), and canopy height (CH) were critical indicators influencing biodiversity. The response curves of the NDVI and CH were positively correlated with the probability distribution of indicator species, while the response curve of the HA showed an overall negative correlation with the same distribution. (2) The spatial distribution characteristics of the ecological network revealed a ‘one axis, two cores, intersecting’ pattern. Ecological sources were supported by mountainous forests and riverside green spaces, symmetrically distributed on both sides of the Yangtze River. Ecological corridors were forming continuous tree belts along highways and riverways, predominantly concentrated on the eastern side of the Yangtze River. Ecological pinch points and barriers were primarily located at the intersections of fragmented green spaces and developed areas in the northeastern and southeastern regions of the study area. (3) This study finally identified 30 ecological source areas, 65 ecological corridors, 8 pinch points, and 8 barrier points. This study presents a construction paradigm for urban ENs from the vantage point of biodiversity conservation, including both regional specificity and universal applicability, providing vital theoretical underpinnings and pragmatic insights for urban sustainability.