In recent years, environmental DNA metabarcoding (eDNA metabarcoding) has been widely used in biodiversity assessment of aquatic organisms due to its cost-effective and non-invasive strategies with the increased sensitivity. To explore new methods for monitoring and detecting jellyfish diversity, this study firstly used eDNA metabarcoding to detect jellyfish diversity of marine aquaculture pond in Liaodong Bay. This study used a standardized process of eDNA metabarcoding analysis, including water collection, water filtration, eDNA extraction, genetic marker amplification, sequencing and bioinformatic analyses. Results showed that all of 8 jellyfish species were detected from 7 sampling sites based on 18S rDNA, including 2 giant jellyfish species and 6 small jellyfish species. A total of 19 jellyfish species were detected from 7 sampling sites based on mitochondrial cytochrome c oxidase subunit I(COI) gene fragment, including 5 giant jellyfish species and 13 small jellyfish species. Only one species (Rhopilema esculentum) was the dominant species based on eDNA metabarcoding. Although eDNA metabarcoding cannot completely replace traditional methods, it can be used as a supplementary tool to efficiently assess and monitor jellyfish diversity and species distribution in the sea. Therefore, eDNA metabarcoding had the technological advantages and could be applied to identify jellyfish biodiversity and detect jellyfish species, and are helpful in early monitoring and warning for jellyfish species in aquatic ecosystems.