Under the pressure of sea level rise and disastrous weather caused by global change, frequency and intensity of coastal hazards such as storm surge, coast erosion, and land subsidence are increasing in China, which requires enhancement of national coastal defense system. Conventional engineering practices of coastal protection are associated with high construction and maintenance cost and difficult to upgrade. Engineering structures have caused severe problems such as land subsidence, water pollution, ecological degradation, and loss of habitats. Ecological engineering based coastal defense provides a new paradigm for protecting coastal communities from natural hazards. Restoration and recovery of coastal ecosystems including beaches, mangroves, salt marshes, and coral reefs provide more sustainable and more cost-effective coastal defense system with tremendous additional ecosystem services. Restoration of vegetation can reduce wave energy, accrete sediment and lift up land surface, which provide adaptation to the hazard risk resulted from sea level rise. Through analyzing the advantages and limits of various types of coastal defense technologies, we argue that ecological engineering should be regarded as a core concept in the construction and management of coastal defense system to achieve optimal operation of socio-economic development and ecosystem conservation.