Abstract: This study aimed to comparatively analyze the effects of live baits and formulated feeds on the structure and function of the intestinal microbiota of mandarin fish (Siniperca chuatsi), thereby providing a theoretical basis for domestication of this species to accept formulated feeds. Metagenomic sequencing was employed to analyze the composition, diversity, and functional differences of intestinal microbiota between the live bait-fed group (HE group) and the formulated feed-fed group (SE group). Results indicated that bacteria constituted the highest proportion (90.74%) of intestinal microbes in the HE group, whereas bacteria and fungus were more predominant in the SE group, accounting for 56.41% and 31.24%, respectively. The dominant phylum in the intestinal bacterial community of the HE group was Proteobacteria, and the dominant viral species was Astyanax_tetra_cavefish_adintovirus. In contrast, in SE group, Tenericutes was the dominant phylum in the intestinal bacterial community, and Cassava_common_mosaic_virus was the richest viral species. Agaricus_bisporus was the dominant fungal species of both groups. The richness and diversity indices of intestinal microbiota were higher in the HE group than that in the SE group, but the difference was not statistically significant (P>0.05). Kyoto encyclopedia of genes and genomes (KEGG) functional analysis revealed no significant differences (P>0.05) between the two groups in pathways such as global and overview maps, carbohydrate metabolism, translation, energy metabolism, membrane transport, replication and repair, amino acid metabolism, and signal transduction. Firmicutes and Proteobacteria contributed more significantly to metabolic pathways, biosynthesis, and signal transduction in the HE group, whereas Tenericutes and Ascomycota played more prominent roles in the SE group. The findings demonstrate that the intestinal microbial composition and dominant flora in the SE group differ from those in the HE group, thereby influencing intestinal metabolic pathways, biosynthesis, and signal transduction. This suggests the potential to indirectly modulate gut functions by altering the nutritional composition of feed.