Artificial reefs are frequently deployed in marine ecosystems to increase fishery yields and enhance the production of reef-associated fauna. However, information regarding trophic structures and pathways of faunal assemblages in artificial reef ecosystems in Pearl River Estuary were still in scare. To this end, we compared the abundances and isotopes of functional groups of fishes and macroinvertebrates in three offshore islands, including Wanshan Island with shallow artificial reefs, Miaowan Island with deep artificial reefs, and Wailingding Island with no reef. The results showed that high connection between pelagic and benthic origin in Wanshan and Wailingding Islands, with pelagic production dominating in Wanshan Island and benthic production dominating in Wailingding Island, respectively. The δ13C value of fishes was significantly lower in Wanshan Island compared to Miaowan Island and Wailingding Island, whilst the δ 15N value of macroinvertebrates was highest in Miaowan Island. Based on the trophic niches, Wanshan Island displayed higher trophic diversity and lower trophic redundancy in fish assemblages, while Miaowan Island was the same in macroinvertebrate assemblages. In addition, four key environmental indicators (i.e., salinity, pH, phosphate, and chemical oxygen demand) and five key environmental indicators (i.e., depth, dissolved oxygen, chlorophyll a, total phosphate, and transparency) were the best at explaining the niche variation of fishes and macroinvertebrates, respectively. Our findings provide an understanding of ecosystem functioning within and around the artificial reef systems to further enhance effective management.