To assess the Siberian crane (Grus leucogeranus)’s response to changing water levels and habitat quality at Poyang Lake, we analyzed the lake’s hydrological trends over the past two decades with the Mann-Kendall and Sen slope methods. Additionally, we explored the link between the crane population size and hydrological conditions at the lake from 2011 to 2019. Meanwhile, five environmental factors, including habitat type, distance from shallow lakes, human footprint index, elevation and normalized vegetation index were selected, and the distribution patterns of suitable habitats for the Siberian crane under 10 water level gradients with intervals of about 1 m (5.3–14.2 m) were simulated by using an improved habitat suitability index model that determines the weights of evaluating factors based on the MaxEnt model. The results showed that the overall trend of the inundated area in Poyang Lake was shrinking in the last 20 years, with a significant increase in the area of exposed floodland during the early wintering period (Z = −2.26). The prolonged drought resulting from this will force vegetation succession, thereby diminishing the food resources for cranes in their natural habitat. The mean inundated area in June demonstrated a significant negative correlation with the population of Siberian cranes in natural habitats (r = −0.75, p = 0.02). Shortage of the Siberian crane-preferred Vallisneria tuber due to June flooding was the primary driver of the crane’s altered foraging strategy and habitat shift. In years with relatively normal June inundation, indicating abundant Vallisneria resources, the relationship between the inundated area during the dry season and the crane population fit well, with a quadratic curve (R2 = 0.92, p = 0.02). The dry season’s inundated area primarily affected the crane population and distribution pattern by influencing the availability of food resources, and both excessive and insufficient inundation areas were unfavorable for crane survival. The modeling results for habitat suitability indicated that as the water level decreased, the trend of the area of good habitat for the Siberian crane showed an inverted bell shape, peaking at a water level of 8.8 m, with optimal conditions occurring between 8 and 10 m. The combined effects of climate and human activities have made the shortage of food resources in Poyang Lake the new normal. The degradation of natural habitats has led to a decline in the quality of Siberian crane habitats, and artificial habitats can only be used as refuges to a certain extent. Thus, formulating strategies to restore natural habitats and enhance the management of artificial habitats is crucial for the conservation efforts of Siberian cranes.