Abstract: The study conducted in October 2022 investigated the macrobenthos community structure and diversity in the Miaodao Archipelago area of the Bohai Strait utilizing environmental DNA metabarcoding (eDNA). A comparison was made between the detection efficacy of eDNA and traditional morphological classification methods on macrobenthos, while also analyzing the primary environmental factors influencing the composition of macrobenthos. 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. Significantly different macrobenthos composition and diversity were observed between the two methods, with eDNA exhibiting a higher species identification at the phylum and genus levels, along with a greater Margalef richness index, albeit lacking in annotating 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 potential of eDNA as a novel biodiversity monitoring tool for effective monitoring of macrobenthos, and suggests its integration with traditional morphological classification for a holistic understanding of marine invertebrates and biodiversity within the region.