Abstract: This study, conducted in October 2022, investigated the macrobenthos community structure and diversity in the Miaodao Archipelago area of the Bohai Strait utilizing the technology of environmental DNA metabarcoding (eDNA). The detection efficacy of eDNA and traditional morphological classification methods on macrobenthos was compared and the primary environmental factors influencing the composition of macrobenthos were explored. The findings revealed a detection of 223 Amplicon Sequence Variants (ASVs) representing 12 phyla, 19 classes, 43 orders, 88 families, and 110 genera of macrobenthos based on 18S rDNA across 16 stations in the waters of the Miaodao Archipelago. Annelids, platyhelminthes, and mollusks were identified as the predominant taxa. Conversely, morphological assessment detected 7 phyla and 68 genera, with annelids and mollusks as the dominant taxa. Significant difference was observed in both composition and diversity of macrobenthos from the above two methods. Environmental DNA can identify more species at the phylum and genus levels, along with a greater Margalef richness index, but can not annotate arthropod crustaceans. The macrobenthic community structure in the Miaodao Archipelago waters was primarily influenced by bottom water salinity, sediment grain size parameters (MD_φ, SK_φ), and TOC content. The study underscores the high potential of eDNA as a novel biodiversity monitoring tool for effective monitoring of macrobenthos, and suggests that its integration with traditional morphological classification, it can comprehensively understand the species and biodiversity of macrobenthos in the region.