Coastal zone is the critical zone of economic development and also the sensitive area affected by land-sea interaction stresses. Rapid urbanization and industrialization have led to various coastal ecological security issues, such as the degradation of key ecosystem services, the disorder of ecological network pattern, and the shrinking of natural habitats for rare species. Based on the theory of land-sea integration,we evaluated the ecological vulnerability from the perspective of "multiple species habitats scales", established the ecological protection and restoration network on the species level, and developed "one map" of coastal ecological security by integrating land-sea ecosystems in the coastal zone of Xiamen-Zhangzhou-Quanzhou megalopolis. Our results are followed:(1) the vulnerability of mangrove and waterfowl habitat had significantly increased due to the highly intensive reclamation, and the high vulnerable areas were mainly concentrated in Jiulong River Estuary, Tong'an Bay and Quanzhou Bay; (2) The ecological security network was consisted of 12 waterfowl migration corridors and 11 ecological nodes, including 4 ecological nodes affecting ecological security of land-sea integration and 3 early warning ecological nodes; (3) The resilient habitats in coastal zone (areas with densely low fragile habitat of waterfowl, amphioxus and Chinese horseshoe crabs) were distributed in Yunxiao mangrove reserve, the nearshore of Dongshan Island, Jiulongjiang Estuary, Dadeng sea area of Xiamen, Weitou Bay, and Shenhu Bay. Our study can provide theoretical supports and integrated solution for designing a resilient coastal zone with the vulnerable coastal ecosystem and rare species, protecting the ecological security of land-sea integation.