Identifying the pivotal factors and their interconnections within the structural, procedural, and functional dynamics of marine ecosystems, which impact human welfare, lays the groundwork for establishing marine environmental management policies closely linked to ecological change and human well-being. Providing targeted regulation of marine ecological damage based on these policies will contribute to realizing the sustainability of marine ecosystem services and achieving the goal of harmonious coexistence between humans and nature. Focusing on the development of a theoretical framework for the management of the marine environment that links changes in marine ecology, human well-being and management policy responses, an ecological production functions were constructed to establish a causal link between ecological inputs and service outputs, which depict the relationship between marine ecological damage and changes in human welfare. Ecological production functions describe the impact of changes in ecological factors resulting from natural conditions or human activities on the supply of final ecosystem services. Changes in ecosystem components and structure affect ecosystem processes, which trigger changes in the provision of ecosystem services. These changes in the supply of final ecosystem services can lead to changes in their value, thus affecting human well-being. On the top of that, some indicators are selected to characterize marine ecological damage, including marine biological resource elements represented by plankton, swimming organisms, benthic organisms, and others, representative elements of marine environmental quality represented by pollutant concentrations and hydrodynamic indicators, and elements of marine biodiversity represented by habitat area and species and functional diversity. Marine ecological damage indicators can define and measure biophysical features of ecosystems that directly affect human well-being, facilitating social explanations of ecological conditions. Both monetary compensation and ecological restoration approaches are chosen to promote the establish of an ecosystem-based marine management system. Marine ecosystem restoration aims to maintain the non-degradation of marine ecosystem services at the macro level. The monetary compensation standard for marine ecological damage is based on the theoretical foundation of maximizing socio-economic welfare and follows the logic of value determination, value loss, and value compensation to calculate compensation for ecological damage, aiming to make up for the loss of personal welfare caused by damage to the marine environment. Research findings can help to build a causal chain from marine ecological damage indicators to compensation policies, which can provide standardized and operational technical support for the identification of marine ecological damage responsibility, selection of monetary compensation, and ecological restoration schemes.