Abstract: Based on multisource observational data, including meteorological records and satellite remote sensing from 1964 to 2020, this study examines Caohai, an inland lake on the Yunnan–Guizhou Plateau designated as a National Natural Reserve, to investigate local climate variations and changes in wintering black-necked crane populations during fluctuations in the lake’s water area. The results indicate that over the past 60 years, the water area of Caohai has undergone five distinct phases: a drainage period, a low-water period, a fluctuation period, a stable period, and a rising period. During stable and rising periods, moisture-related factors showed stronger correlations with changes in water area than thermal factors did. Across all five phases, air temperature patterns in surrounding regions were generally consistent with those in the Caohai area, with 37% of meteorological stations showing a similarity index of 1.0. Climatic variations in downstream precipitation to the east and wind speed in the northwest direction were also consistent with changes in the Caohai region. The population of wintering black-necked cranes varied significantly across different water-area phases, with low water-area periods corresponding to lower crane populations. These findings demonstrate that changes in the water area of Caohai are synchronous with climatic variations in surrounding meteorological elements. Furthermore, maintaining an adequate water area is critical to preserving the quality of wintering habitats for black-necked cranes