Against the backdrop of rapid urban expansion, preserving landscape connectivity has become a vital approach to addressing habitat fragmentation and enhancing biodiversity. This study takes Chongqing, China, as a case study and establishes a multi-scale evaluation framework encompassing the Main urban area-Main metropolitan area-Chongqing city. Using landscape connectivity indices and ecological security patterns, the study evaluates the structural and functional connectivity of the research area. Through comparative analysis, it demonstrates the scale-dependent differences in regional landscape connectivity and proposes protection strategies from a multi-scale perspective. The results indicate that in terms of structural connectivity, as the study scale expands, the dPC (Delta Probability of Connectivity) rankings of all core areas within the urban core significantly decline, while those in Jiangjin, Nanchuan, and Fuling districts within the metropolitan area experience significant degradation, moderate degradation, and upgrading, respectively. In terms of functional connectivity, the corridors (394.79 km²) and source areas (39.61 km²) in Beibei, Yubei, Nan’an, and Banan districts are crucial for landscape connectivity protection at small- to medium-scale levels, while the corridors (11.33 km²) and source areas (1,180.41 km²) in Nanchuan and Fuling districts are pivotal for connectivity protection at medium- to large-scale levels. This study provides systematic and comprehensive strategic references for the protection of landscape connectivity.