Abstract: Global warming severely affects the continuity and suitability of habitats for endangered waterbirds. It is of great significance to investigate the habitat selection of Aythya baeri and its influencing factors in the context of climate change, and to explore its conservation gaps. We used an ensemble of the generalized linear model (GLM) and maximum entropy (MaxEnt) model, combined with three evaluation metrics—AUC, TSS, and the continuous Boyce index—to predict the current and future potential suitable habitats of Aythya baeri in China under multiple climate scenarios. These predictions were then overlaid with China's national nature reserve network to assess conservation gaps. The results showed that the total current suitable habitat area for Aythya baeri was 200.82×10⁴ km², accounting for 20.9% of China's total land area. Of this total, the low-, medium-, and high-suitability areas were 132.73×10⁴ km², 47.25×10⁴ km², and 20.84×10⁴ km², respectively. The high-suitability areas were primarily concentrated in the middle-lower Yangtze River Plain, the eastern North China Plain, the Bohai Rim coast, and the Sichuan Basin. The dominant environmental variables driving the model predictions were isothermality, precipitation of the driest month, annual mean temperature, and elevation, with contribution rates of 14.5%, 11.3%, 10.7%, and 10.2%, respectively. The overall centroid of the suitable habitat shifted southwestward toward Hubei Province but remained within Henan Province. The conservation gap showed a slight decreasing trend; however, the current protected area network covers only approximately 6.76% of the high-suitability habitat. Accordingly, it is recommended to establish wetland parks or small seasonal protected areas within the conservation gaps of the transitional zone between North China and Central China, thus improving the protection coverage of highly suitable habitats and achieving targeted conservation.