Based on the field survey and reference data of the sea area of the Zhongjieshan Islands from 2021 to 2022, the Ecopath model was used to analyze the energy flow structure of the marine ecosystem of the sea area of the Zhongjieshan Islands; the energy structure of the marine ecosystem was divided into 21 functional groups, and its nutrient structure, energy flow, and total system characteristics were analyzed. The results show that the credibility of the model is 0.414, which is at a medium level. The trophic level of each functional group of the ecosystem in the sea area of Zhongjieshan Islands was 1–3.48, the energy flow structure of the system was mainly concentrated in the first five grades, and the trophic level was relatively simple, with the average energy transfer efficiency of the system being 8.11%, the energy flow range being 2.81–13.04%, the energy transfer efficiency of the primary producers of the system being 7.25%, and the energy conversion efficiency of the system debris being 9.12%. The total system throughput was 2125.96 t·km−2; The analysis of the overall characteristics of the ecosystem showed that the system connectance index and the system omnivory index were 0.45 and 0.24, respectively, while the Finn’s cycling index was 8.24, the Finn’s mean path length of the system was 2.72, and the total primary production/total respiration was 1.71. In this study, the marine ecosystem model of the sea area of the Zhongjieshan Islands was studied to understand the trophic structure and ecosystem status of the sea area, which is conducive to the sustainable utilization and scientific management of fishery resources in the sea area.
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