Green sea dykes, also known as ecosystem-based sea dykes, represent a novel type of coastal defense consisting of both traditional structural engineering and coastal ecosystems, designed to cope with the future trends of sea level rise and intensified storms. Here we focus on the mid-latitude mud coasts (eastern China in particular), which face the most prominent risks of storm surge, storm-induced giant waves, and shoreline erosion, and summarizes the scientific basis of green sea dykes and the current status of engineering practices. We show that the basic mechanisms of nearshore wave energy dissipation include bottom friction, sediment transport, and form drag. These explain the wave damping capacity of oyster reefs and salt marshes on mud coasts. In tidal flat environments, oyster growth increases frictional resistance and even causes wave breaking; the resuspension and transport of fine-grained sediments on salt marsh beds and the movement or resistance to hydrodynamic forcing of salt marsh vegetation stems effectively dissipate wave kinetic energy, and their efficiency increases with the elevation of the bed surface. Based on the wave damping capacity of oyster reefs and salt marshes on mud coasts, ecosystem-based sea dykes are being built in combination with traditional structured sea dykes. By utilizing natural tidal flats outside the dykes or implementing artificial modification projects, a certain scale of salt marshes and/or oyster reefs can be maintained, which serve to protect the sea dykes and enhance their wave resistance functions. From the perspective of system optimization, it is necessary to further improve the efficiency and sustainability of green sea dykes under constraints such as regional environment characteristics, ecosystem health, investment capacity, and ecological resilience. Related scientific issues include the theorization of the wave damping process of salt marshes, the niche and scale control of oyster reef and salt marsh ecosystems, the establishment of engineering standards and the design of the optimal form of sea dykes.