Pampus argenteus demonstrates a preference for Rhopilema esculentum as prey, yet the ramifications of consuming supplemental medusa on fish microbiota and metabolism remain elusive. To elucidate these effects, 300 juvenile fish were divided into two groups: control group (C, given commercial food only) and supplemental medusa (SM) group (given supplemental medusa + commercial feed). After 15 days, fish in the SM group exhibited a significant increase in fatness, the amylase activity in the intestine significantly increased, and the intestinal microvilli were arranged more neatly. The comprehensive approach involving 16S rRNA amplicon sequencing and metabolomics was employed, leading to the identification of five genera within the SM group, namely Lactococcus, Cohaesibacter, Maritalea, Sulfitobacter, and Carnobacterium. Functional prediction analysis of the microbiota indicated that the consumption of supplemental medusa facilitated processes such as glycolysis/gluconeogenesis and amino acid absorption. Metabolomics analysis revealed significant enrichment of 85 differential metabolites, most of them belonging to fatty acids and conjugates. These differential metabolites primarily participated in processes such as amino acid metabolism, fatty acid synthesis, and disease. Notably, the consumption of medusa resulted in a significant reduction in nine lysophospholipids associated with cardiovascular disease and inflammation. Pearson's correlation coefficient analysis revealed associations between specific microorganisms and metabolites, indicating that Cobetia, Weissella, and Macrococcus exhibited an increased abundance in the SM group, positively correlating with apocynin, 12-Hete, and delta 9-THC-d3. The indicator bacteria Psychrobacter reduced in the SM group, exhibiting a negative correlation with cystathionine (a compound involved in glutathione synthesis). Overall, the supplementation of medusa may confer a beneficial effect on the immunity of the fish. This study contributes to the theoretical framework for fish feed development.