Assessing temporal and spatial changes in marine ecosystem assets is critical for the capitalized management of natural resources and their contribution to human well-being. However, quantifying these changes using different inclusion methods in the System National Account is a challenge. Ecosystem accounting has become a popular topic in recent years, particularly after the System of Environmental and Economic Accounting-Ecosystem Accounting was published in 2021. However, few practical studies have been conducted on offshore marine ecosystem accounting, including marine ecosystem assets and services. This study provides a systematic framework to prioritize the assessment of offshore marine ecosystem assets (extent and condition) in physical terms, including the determined indicators of physical accounts and the presentation of accounting results. We then used this framework to assess marine ecosystem assets in the Xiamen Sea Area selected from 2006 to 2020. The results show that: (a) The extent of the marine ecosystem in Xiamen decreased by 8.34% from 349.64 km2 to 320.49 km2, mainly caused by converting intertidal ecosystem into the land due to the demand for urban and industrial use sea. (b) The area of intertidal vegetation habitats (mangroves and salt marshes) increased from 23.22 hm2 to 132.2 hm2, with an increase of 4.7 times. The results also show that the restoration of the marine ecology in Xiamen has achieved remarkable results. (c) The marine ecosystem condition comprehensive index in Xiamen increased by 3.13% from 0.32 to 0.33. This shows that the marine ecosystem conditions in Xiamen remain well and have even slightly improved under the pressure of a rapidly developing economy and increasing population. This study provides practical technical methods for assessing offshore marine ecosystem in physical term to support integrated coastal management in coastal cities, and is important for assessing marine ecosystem services in the future.