Owing to rapid urbanization, coastal regions worldwide are experiencing immense resource and environmental stress. Ecological restoration is vital for maintaining and sustainably developing coastal regions. This study proposed a method for delineating priority areas for ecological restoration based on the social-ecological systems (SES) theory. First, an analytical model was established based on three dimensions: ecosystem function, social system pressure, and SES evolution, for analyzing the social and natural systems of coastal regions. Second, based on the modes of land–sea interaction relevant to ecological restoration, auxiliary marine factors were incorporated to aid the delineation of priority areas for ecological restoration. A case study was conducted on the Dapeng New District of Shenzhen City to validate our method. The marine areas of the Dapeng New District have significantly poorer ecosystem function than its terrestrial areas because of the natural geography of this area and human activities. A total of 43.4% of marine areas require artificially assisted ecological restoration, and inland areas 1.5 km from the shoreline are significant for ecological conservation and restoration. Additionally, estuaries and artificial shorelines should be the focus of ecological restoration work in the study area. This case study proved the efficacy of our method. The findings will serve as a reference for the planning and implementation of ecological restoration plans in coastal regions.