Identifying the important ecological areas for priority protection is critical to conducting the regional ecological security pattern. Taking a typical waterside area in Shanghai Metropolitan Area as a case study, this paper proposed a composite evaluating index framework of land-water ecosystem services (ESs) considering aquatic and terrestrial aspects, based on the ESs supply efficiency and multi-source data. We calculated the supply capacity of aquatic, terrestrial ESs, and land-water coupling degree respectively by quantitative evaluation model and coupling method to extract the vital ESs supply patches as the priority protected areas. Then some hierarchical control suggestions were put forward to determine the protected grades based on the landscape connectivity. The results showed that: (1) The total area of the priority protected areas was 263.37 km², accounting for 12.29% of the whole region, and was mainly distributed in northwest areas more than in the southeast areas. (2) The aquatic and terrestrial priority protected regions were identified with areas of 240.02 km² and 23.35 km² respectively through the land-water coupling analysis. (3) The ecological priority was divided into four grades. (4) The coincidence rate between the planned control line of the study area and priority protected areas was up to 81.12% and the non-coincident part could be used as the priority green spaces for urban planning in the future. The study provides a scientific model for the implementation of ecological space protection and restoration in regions around the metropolis in developing countries.