<p>This study surveyed the Xiaoheishan Island artificial reef area in China’s Bohai Sea (deployed in 2014) through year-round ecological surveys conducted in 2023. Using environmental DNA metabarcoding technology, we systematically studied the ecological restoration effects and underlying mechanisms of the artificial reef area. The results revealed 91 genetically identified fish species in the artificial reef area, compared to 87 species in the control area, indicating that artificial reefs play a positive role in restoring biodiversity. Principal Component Analysis demonstrated significant seasonal and spatial differences in biological distribution between the artificial reef and control areas (<i>P</i>&lt;0.05). Specifically, the artificial reef area is dominated by small demersal rock-associated fishes such as Gobiidae, Scorpaeniformes, <i>Lateolabrax japonicus</i>, and <i>Hexagrammos otakii</i>; in contrast, the control area features predominantly pelagic and soft-bottom species including <i>Liza haematocheila, Engraulis japonicus, Mugil cephalus, Paralichthys olivaceus</i>, and <i>Scomberomorus niphonius</i>. By Canonical Correspondence Analysis, we propose that seasonal migration driven by water temperature and species’ life-history strategies promote habitat partitioning between the artificial reef and control areas, which in turn influences the distribution of dissolved oxygen and NH<Stack> ₄ ⁺ </Stack> in the water. Through the correlation analyses, it is found that although chlorophyll levels were higher in control area, the category and diversity indices of plankton showed marked declines compared to the artificial reef area. We believe that, compared to control areas, artificial reefs can increase the biodiversity of smaller organisms but cannot support large predators and higher biomass.</p>