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Objective The Yancheng coastal wetland in Jiangsu province, as a UNESCO (United Nations Educational, Scientific and Cultural Organization) natural heritage site with an area of 2687 km2, is one of the most important habitats for overwintering of red-crowned cranes in Asia. In recent decades, due to the combined effects of intensive human activities such as industry, agriculture, aquaculture and urbanization, the pattern of coastal wetland system and the suitable habitat for red-crowned cranes have changed dramatically. Therefore, it is a great importance to effectively detect the spatio-temporal variation pattern of coastal wetland system and explore its key impact factors in order to protect the coastal wetland and conserve its biodiversity. At present, the research on land cover change in the Yancheng coastal wetland is insufficient to the species habitat monitoring. It is necessary to conduct further study on the suitable habitat for red-crowned cranes in a long-term and large regional scale. Method In this study, the multi-temporal and multi-source remote sensing data like Landsat TM/OLI data during 1989 to 2019 and Sentinel-2 data in 2019 are used to analyze the features of spatio-temporal variation in the Yancheng coastal wetland. Firstly, the classification system and image interpretation symbols of study area were established to draw the maps of classification and transfer distribution in six periods during 1989 to 2019. Then, the structural and functional connectivity of suitable habitat for red-crowned cranes were evaluated based on the species diffusion ability. Finally, the key ecological nodes for overwintering of red-crowned cranes were evaluated. Result Our results show that the eco-environment of natural wetland has degraded rapidly, with an area loss of 49.46%. In contrast, the artificial wetland increased with 69.24%, which was mainly realized by occupying the natural wetland and reclaiming the tidal flat. The center of reclamation has a tendency of migrating from north to south and from coastal land to sea. The area of seepweed saltmarsh and alkaline land as suitable habitat decreased by 489.10 km2, with a proportion decreased from 19.88% in 1989 to 4.36% in 2019. As for structural connectivity, our results show that the connectance index of suitable habitat patches had decreased from 1.83 to 1.30, showing a downward trend. The distance between the patches increased and the fragmentation intensified. At the same time, the estimations of functional connectivity index show that the integral index and probability index of connectivity in 2019 are both less than 0.01. The functional connectivity has decreased and the connection network is generally broken with only a small part of connection network with high betweenness centrality index. They are existing in the core area of UNESCO natural heritage site and the Tiaozini region. They are also the key ecological nodes for red-crowned cranes habitat. Conclusion In summary, the connectivity of suitable habitat for red-crowned cranes has decreased sharply because of land cover change in the UNESCO natural heritage site--Yancheng coastal wetland in the past 30 years. However, the habitat for red-crowned cranes has been greatly improved since the core area has reverted aquaculture pond and cultivated land to natural wetland in 2014. In addition to enhancing the scientific conservation of the existing suitable habitat like the core area of UNESCO natural heritage site and Tiaozini region, the key ecological nodes in the natural wetland should be restored in order to improve the connectivity among the habitat patches.