Artificial reef is regarded as an effective tool for restoring habitats and supporting the marine ecosystem. While the energy flow and material exchange in the food web of artificial reef ecosystem still remain vacant and should be further understood. In this study, stable isotopic characteristics (δ13C and δ15N) were used to identify the trophic niches and potential carbon sources of consumers (fish and invertebrates) in artificial reef areas and adjacent habitats in Haizhou Bay (the estuary area (EA), the aquaculture area (AA), the artificial reef area (AR), the natural area (NA) and the comprehensive effect area (CEA)) in spring and autumn. The results showed that the average δ13C for all consumers decreased from -16.99 ± 2.07‰ to -21.81 ± 1.66‰, and the average δ15N ranged from 11.37 ± 0.35‰ to 14.69 ± 0.64‰ in all seasons. A SIBER model revealed highly similar trophic niche among habitats in autumn, and lower overlap in spring. The SIMMR model showed that phytoplankton and sedimentary organic matter (SOM) were the major contributors to consumers, and particulate organic matter (POM) accounted for less contribution. In AA and NA phytoplankton and SOM generally contributed fairly equally to most fish, while single SOM sources were major contributors to nearly all the species in AR and CEA. Our findings reveal that ARs can serve as seascape mosaics to increase fish community diversity because of their high variation in the δ13C value and the trophic niches from EA to the NA. Preliminary multidisciplinary studies are needed for the mitigation of effects before any implementations deployed to the offshore waters that influence habitat connectivity, especially some habitat–specific migratory species.