Abstract: The Chongqing Three Gorges Reservoir area is rich in species resources and diverse in habitat types. The construction of a habitat network may further promote species migration and exchange between regions, which is of great significance for maintaining biodiversity. Through the comprehensive application of MSPA-InVEST model, MaxEnt model, and minimum cumulative resistance model, this study identified and optimized the habitat network in the Chongqing Three Gorges reservoir area and proposed protection strategies. Firstly, the MaxEnt model was used to identify the key areas of bird habitat and determine the main environmental factors affecting bird distribution, including isothermal, average temperature of the wettest quarter, and land use type. Then, the spatial morphological characteristics of habitat sources were analyzed by the MSPA-InVEST model. Finally, the bird habitat network was constructed by the minimum cumulative resistance model to optimize the corridor layout. The results showed that there was significant spatial heterogeneity in the habitat network in the Chongqing Three Gorges Reservoir area, and the habitat quality and connectivity of birds in different regions were significantly different. Based on this, the regional protection measures were put forward to improve the implementation effect of regional biodiversity protection.