The landscape of the Poyang Lake wetland is significantly influenced by changes in water levels, impacting the distribution of habitats for migratory birds. While long-term effects of water level variations have been extensively studied, short-term impacts on Siberian crane habitats and their ecological vulnerability remain poorly understood. This study utilized 35 years (1987–2022) of Landsat remote sensing data and daily water level records from Poyang Lake to examine the effects of short-term water level fluctuations on the spatial distribution and ecological vulnerability of Siberian crane habitats. The geographic detector method was employed to quantify the explanatory power and interaction effects of factors, including short-term water level fluctuations, on ecological vulnerability. The findings reveal significant differences in the habitats of wintering Siberian cranes across various water level intervals and short-term fluctuation patterns. Short-term water level fluctuations can result in the largest suitable wintering habitat area for Siberian cranes, reaching 1856.41 km² in this study. These habitats are highly sensitive to short-term water level changes, with rising and falling trends potentially leading to habitat loss. Oscillating water levels in the short term create broader and more concentrated habitats. Notably, fluctuations at low water levels support the sustainability and stability of crane habitats. Furthermore, short-term water level trends and nature reserves play a critical role in maintaining habitat ecological vulnerability; well-managed and protected nature reserves exhibit significant explanatory power, both in single-factor analysis and in their interaction with other environmental factors. Specifically, these protected areas show explanatory power exceeding the 20% threshold for both water level fluctuations and ranges, highlighting the crucial role of anthropogenic management in mitigating ecological vulnerability. This study emphasizes the necessity of scientifically informed regulation of short-term water level fluctuations to protect Siberian crane habitats and provides a strong scientific basis for decision-making support.