There is extensive material migration and energy exchange between land and sea. Land–sea integration management is an important principle for the economic development, resource utilization, spatial layout, environmental protection and ecological security of the land and sea system, which requires to establish an integrated ecological protection system, and maintain the healthy ecosystem and sustainable economic development. The estuary plays an important role for land–sea integration. The characteristics of estuary, such as hydrodynamic force, aquatic ecology and geographical position, determine the importance of its ecological environment to human activities. However, the existing problems were considered in estuarine, including ambiguous of estuarine administrative boundary, insufficient monitoring, and unapplicable water quality criteria. Under the background of accelerating national land and space coordination, in order to achieve the land–sea ecological protection, it is necessary to break the region boundaries and policy management barriers, form an integrated management for healthy ecosystem structure and function. Therefore, policy recommendations for estuarine management under the land–sea integration were put forward, such as demarcating the estuary boundary, putting forward estuarine ecological environment assessment system, implementing watershed–estuary–offshore collaborative pollution control, and establishing intelligent supervision platform, which will strengthen the estuarine ecological protection.