Marine ecosystem hold immense economic and ecological value. They have great significance to global ecological security and human well-being through sustainable utilization and management. How to regard marine ecosystems as quantifiable and manageable "assets" and integrate them into the framework of natural resource assetization management, promoting the conversion of "lucid waters and lush mountains" into invaluable assets are key pathways to achieving their scientific conservation and sustainable utilization. Understanding the temporal and spatial variation of marine ecosystem asset is essential for implementing natural resources assets management and evaluating their contribution to the people. As an important source of information for understanding the spatial distribution and quality of marine ecosystem assets, physical accounting serves not only as the first step in the full process of marine ecosystem accounting, but also as a data foundation for subsequent marine Gross Ecosystem Product (GEP) accounting. Using the marine ecosystem accounting area in Xiamen as a case study, this research presented changes in marine ecosystem assets based on physical accounting over the past fifteen years, including marine ecosystem extent and marine ecosystem condition. The accounting results reflected the effectiveness of marine ecosystem restoration practice and comprehensive management in the accounting area. Then we presented the bottleneck in marine ecosystem assets physical accounting from basic data, transformation and application, and system mechanism. This article provided some recommendation: (a) It was necessary to strengthen the supporting role of basic data and fix the statistical caliber of data, aiming to implement regular physical accounting of marine ecosystem assets. (b) It was necessary to establish a data accounting platform to effective link the account of marine ecosystem assets accounting with the national economic accounting account, aiming to provide support for the subsequent scientific and reasonable allocation of marine ecological compensation funds. (c) It was necessary to speed up the improvement of relevant systems and mechanisms for the marine ecosystem assets accounting, aiming to provide institutional guarantees for the subsequent development of marine ecological compensation and market-oriented transactions. Inspired by research on marine ecosystem assets physical accounting, the article provides insights into the management of nartural resources assetization. It aims to accelerate the promotion and lay the groundwork for management decisions and research related to the audit of natural resource assets upon the departure of leading officials in coastal cities of China, as well as the gross marine ecosystem product accounting and its value realization. Furthermore, it ultimately contributes to the Ecological Civilization Construction in China.