Marine ecosystem assets accounting is a cornerstone of the marine resource assets management; however, it is facing an imperfect accounting system in the current situation. Based on the System of Environmental Economic Accounting (SEEA) Experimental Ecosystem Accounting, this paper initially combines the key concepts, the objectives, the extent, and the tabular structure in measuring the ecosystem assets. Subsequently, with the marine ecosystems as the research object, this paper attempts to design the accounting tables for the marine ecosystems extent, marine ecosystems conditions and the expected service flows of the marine ecosystems in physical terms. Furthermore, the technical issues such as trade-off, pricing and the choice of asset discount rate on expected marine ecosystem services are explored. With the accounting of the expected marine ecosystem services in monetary terms, the calculation of the marine ecosystem assets using the net present value method is possible, and the marine ecosystem assets accounts can be compiled. Finally, this paper proposes the existing challenges and directs the need for further research in designing the framework of marine ecosystem assets accounts.