The endangered red-crowned crane (Grus japonensis, RCC) has the smallest population of all Chinese cranes, and is also susceptible to climate change because of its large body size, short migration distance, and specialized diet. We examined climate change-induced RCC habitat shifts and suggested some purposeful, resolute and crucial improvements needed to protect appropriate areas that ensure the RCC’s long-term survival. Based on monitored data of nesting locations and climate variables gathered from 2014 to 2017 around Zhalong Reserve on the Songnen Plain in northeast China, we used four General Circulation Models in Maxent modeling to project changes, including suitability and fragmentation, in RCC breeding habitat up to the year 2050. Based on climate change, we predicted a decline in 2050 of suitable and sub-suitable habitat from the current 26.2% to 14.3%-19.7% in the study area, but an even larger loss (from 71.3% to 27.3%-32%) of suitable habitat in Zhalong Reserve. The predictions also showed a northward movement of RCC habitat and a loss of current suitable habitat southeast of Zhalong Reserve, resulting in a discrepancy between future habitat areas and currently protected areas. In addition, climate change will further fragment RCC habitat, thus decreasing habitat suitability and carrying capacity, especially within Zhalong Reserve. Our study indicated that the most suitable breeding habitat is currently restricted to the Reserve. This finding partially explains that the low rate of RCC population growth is likely because of the limit of RCC’s expansion due to spatial patterns of suitable habitat. We confirmed that temperature, rather than precipitation, had the most impact on RCC breeding. To cope with climate change, we recommend that new refuges be designed within the study area and the transformation of wetland to farmland in the area be banned. Also, organic agriculture methods and crop species that consume less water than rice should be adopted to mitigate the adverse climate changes that accompany global warming and will contribute to RCC habitat degradation.