Recently, under the impacts of environmental shifts and human activities, marine ecosystem conservation and recovery have become increasingly important for the management and sustainable development of fishery resources. We construct two Ecopath models to describe and compare the similarities and differences in the structure and function of the ecosystems in Haizhou Bay (HZB) for 2020–2021 and Lvsi Fishing Ground (LSFG) for 2018–2019 in this study. Our results highlight the similarities of the two ecosystems in which plankton (e.g., zooplankton and phytoplankton) are important functional groups with bottom-up effect control and congers control the top-down effect. The differences between the two ecosystems indicate that the HZB ecosystem is relatively mature due to higher Finn’s cycling index (FCI), Finn’s mean path length (FMPL), Connectance Index (CI), System Omnivory Index (SOI), and Ascendency/capacity (A/C). However the food web structure in the LSFG is more diverse and stable with higher Overhead/capacity (O/C) and Overhead/capacity (H). The differences are possibly due to the low trophic level (TL) species composition in the two ecosystems. Therefore, we suggest that stock enhancement and release methods should be deployed to release high TL species into designated water areas to increase food web complexity and ecosystem maturity in HZB and LSFG. This study will help inform ecosystem and fishery regulations in different ways and facilitate discussion towards the establishment of strategic conservation planning and adaptive management.