For many years, jellyfish were described as ‘dead ends’ in marine food webs, due to their high-water content and low nutritional value. However, it has been confirmed that silver pomfret (Pampus argenteus) has a particular preference for preying on jellyfish. In this study, we determined the effect of consuming jellyfish on the intestinal microbes of silver pomfret. Analysis of bacterial 16S rRNA gene amplicons showed that jellyfish had a dramatic impact on the composition of the gut microbiota. The content of Proteobacteria was reduced from 99% to 51%, while Firmicutes, Bacteroidetes and Actinobacteria increased, accounting for 35%, 9% and 2% of the total flora, respectively. At the genus level, the content of Photobacterium decreased sharply to <1% of the total flora. By contrast, Lactobacillus, Burkholderia and Sphingomonas increased to 12%, 9% and 7% of the total flora, respectively. After feeding jellyfish, the functions of intestinal microbes and the activity of digestive enzymes also changed, resulting in better digestion and absorption of jellyfish. The results provide insights into the specific bacterial taxa within the silver pomfret intestinal microbiome that are impacted by jellyfish. Silver pomfret can better digest and absorb jellyfish by adjusting the intestinal microbial composition. The findings provide a theoretical basis for the digestive mechanism by which silver pomfret consume jellyfish.