In recent years, under the mutual influence of the rapidly changing offshore environment and human activities, the management and sustainable use of fishery resources has become increasingly important for protection and restoration of marine ecosystems. In this study, Ecopath models of artificial reef ecosystem (ARE) and estuary ecosystem (EE) in Haizhou Bay were constructed according to fishery resource data in 2020-2021. The differences and similarities in structure and function of food webs in the two areas were described and compared. The results showed that the biomass flow of ARE was directly or indirectly derived from the detritus food chain. The trophic level I-III accounted for more than 97.98% of the total biomass flow of the ecosystem, and the biomass flows of EE was derived from the primary productivity food chain, with trophic level I-III accounting for more than 99.88% of the total biomass flow. Plankton is an important structural functional group with bottom-up control effect, while top predators control the top-down effect of the two ecosystems. Generally, EE is more mature than ARE 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) values, but ARE has higher Overhead/capacity (O/C) and Shannon diversity index (H) values, and the food web structure is more diversified and stable. It is concluded that the continuous construction of artificial reef will help enhance fishery resource recovery and promote the ecosystem of Haizhou Bay to a more mature, stable and healthy status.