Climate change and human activities have an essential impact on the distribution and survival of critically endangered species. Here we used the ENMeval-optimized MaxEnt model to simulate the potential habitat of the endemic and critically endangered species Alligator sinensis in China under the future climate scenario of CMIP6. We identified the main environmental factors affecting the geographic distribution of Alligator sinensis by Jackknife test and analyzed the response of the species' geographic distribution to these environmental factors. The results show that the coldest quarterly precipitation (Bio19), the driest quarterly mean temperature (Bio9), the wettest monthly precipitation (Bio13), elevation, and the seasonal coefficient of temperature change (Bio4) are the most important environmental factors influencing the distribution of Alligator sinensis. The coldest quarterly precipitation of 132.12-156.84 mm, the driest quarterly average temperature of 5.94-7.81℃, the wettest monthly precipitation of 180.44-221.65 mm, the elevation of 4.60-121.69 m, and the seasonal variation coefficient of the temperature of 872.08-903.30 are the most suitable environmental conditions for the survival of Alligator sinensis. Human activities would cause the reduction of the habitat range of wild Alligator sinensis. Under different climate change scenarios in the future, the suitable habitat of Alligator sinensis will be larger under the SSP126 climate scenario than the SSP585 climate scenario, and the sustainable development path of low vulnerability and low radiative forcing can slow down the loss of suitable habitat of Alligator sinensis. Based on the modelled results, wild release sites or new natural reserves can be established in Yixing, Jiangsu Province, and Dongting Lake Plain, Hunan Province. Our study provides a scientific guide to the wild release and genetic diversity conservation of Alligator sinensis.