The Siberian crane (Grus leucogeranus), a critically endangered species, is used as an indicator species for ecosystem stability because of its sensitivity to the environment. The distribution of Siberian cranes has shown dramatic fluctuations on an order of magnitude at the main stopover site (Jilin Momoge National Nature Reserve) since the present century, which poses a great challenge to the conservation of endangered species. Research on the threshold values of key factors of the Siberian crane in stopover habitats and the relationship between the Siberian crane and hydrological temporal and spatial fluctuations can promote endangered species conservation. The response of population changes and distribution patterns of Siberian cranes to hydrological temporal and spatial patterns of wetlands was analyzed from 1984 to 2020. The results showed that population changes and distribution patterns of Siberian cranes were highly correlated with hydrological temporal and spatial patterns in the study area, and their variation trend was the same. However, there were obvious stage migration changes in the core activity area of the Siberian crane (1984-2000, 2001-2010 and 2010-2020). The habitat characteristics of fragmentation, dispersion and complex shape of water bodies changed from steady to dramatic fluctuations and then leveled off in the core activity area of Siberian cranes during the 37 years of migration transit. This was closely related to the early agricultural reclamation and the later ecological water replenishment project in the study area. In addition, the trend of the water pattern index of the spatial distribution of Siberian crane active habitat was also closely related to their habitat selection preference. When the perimeter area fractal dimension of water (1.27-1.30), landscape division index (0.73-0.95) and aggregation index (80.97-91.36) are within a certain stable threshold, the stopover habitat of the Siberian crane is suitable.