Abstract: The loss and fragmentation of suitable habitat in the wild is the biggest challenge for the protection of Chinese alligator. Building and maintaining the ecological corridor between habitats is an important protection strategy. Taking 8 blocks of the Chinese Alligator Nature Reserve as the ecological sources, this study aimed to build a comprehensive resistance surface, to simulate the ecological corridors between blocks, to identify the ecological “pinch points” and “barriers”, and to propose targeted protection and repair strategies. The Linkage Mapper tool and the Circuitscape program were used in this study. The research results were as follows: (1) There were 14 identified ecological corridors with a total length of 391.06 km, which were in the state of “long in the east and short in the west”. Seven key ecological corridors effectively connected Changle, Zhongqiao, Shuangkeng and Hongxing areas in the southwest of the study area; (2)12 ecological pinch points were identified, with an area of 82.35 km2. The protection strategy of giving priority to natural protection, supplemented by the creation of suitable habitat for Chinese alligator was put forward. At the same time, attention should be paid to the risk of certain pinch points that was disturbed by human activities; (3)19 ecological barriers were identified, with an area of 92.49 km2. It was mainly located in traffic trunk lines, urban land or surrounding radiation areas. Suggestions such as setting up animal migration channels, promoting ecological agriculture, optimizing the layout of residential areas, and resolving the conflicts between people and alligators were put forward.