The great lake basins serve as critical migration corridors and habitats for birds, but their habitat quality is seriously threatened by land use change. However, how the sensitivity of bird habitat quality to land use change varies across the great lake basins in different climatic zones remains unclear. In this study, 56 great lake basins in China were classified into four climatic zones: the Temperate Monsoon Zone (TM), the Mountainous Plateau Area (MP), the Temperate Continental Arid Climate Zone (TCA), and the Subtropical Monsoon Zone (STM). Differences in the sensitivity of bird habitat quality to land use change were identified. Changes in bird habitat quality across multiple biodiversity hotspots within the great lake basins were simulated using CMIP6 scenarios. The results showed that bird habitat quality in the STM great lake basins was highly sensitive to changes in water bodies, whereas the other basins were more sensitive to changes in grassland. From 1990 to 2020, bird habitat quality in the MP, TM, and STM great lake basins decreased by 18.61%, 15.97%, and 15.02%, respectively. Although the bird habitat quality in the TCA great lake basins increased by 6.00% between 1990 and 2020, it faced the highest risk of decline under future scenarios. The most significant degradation occurred in three biodiversity hotspots: the Altai Mountains, the Southwestern Tien Shan-Junggar Basin, and the QiangtangSanjiangyuan area. From a multi-climatic-zone perspective, this study examines the differential responses of bird habitat quality in the great lake basins to land use change, providing actionable insights for targeted bird habitat conservation in these regions.