Approximately 70% of the world’s largest megacities (>10 million people) are within 60 km of the coast, contributing to 50% of the world’s GDP. Sea level rise will intensify coastal flood threats, making cities without sufficient habitat protection even more vulnerable. However, there is currently a lack of thorough evaluation at the global coastal scale about conservation priorities based on the current habitat cover and the high sea level rise in order to adapt coastal flood risks. Here we assessed the disparity among habitat coverage, exposed population and extreme sea level rise to identify priority areas for future conservation. These priority areas are characterized by a large population residing in low-elevation coastal zones (LECZs), high extreme sea levels (ESLs), and insufficient habitat coverages. In many highly populated countries like China and India, the flooding risk has been underestimated due to insufficient adaptation based on natural processes from coastal habitats. These highly populated countries are especially concerning because they have comparatively less vegetation protection capability and are subjected to high ESLs. Globally, Asian and European nations, such as China, Japan, Bangladesh, Viet Nam, the United Kingdom, Belgium, Ireland, the Netherlands, and Germany, rank highest for natural climate solutions conservation. We found that the main contributors to variations in the extreme sea level rise risks are not due to exposure headcounts (6%), but due to inadequate habitat cover (42%), which can be improved through targeted conservation and restoration. Our research identified the global priorities for managing climate resilience that most urgently require ecosystem conservation and restoration in order to prepare for the risks of coastal flooding.