Abstract: Red spot disease is the most prevalent bacterial disease in sea urchin (Strongylocentrotus intermedius) aquaculture, exhibiting rapid development, high contagion and a considerable mortality rate. We investigated the gut bacterial community composition and function characteristics of sea urchins with red spotting disease by using 16S rRNA sequencing technology, so as to reveal the correlation between diseases and gut bacterial communities. The results demonstrate that compared with the healthy sea urchins, the number of operational taxonomic units (OTUs) and the Alpha index in the gut microbiota of the diseased ones decreased significantly (p<0.05). On phylum level, the relative abundance of Proteobacteria and Bacteroidota in the gut of diseased sea urchin increased significantly, while the relative abundance of Firmicutes was significantly lower (p<0.05). On genus level, the relative abundance of Burkholderia_Caballeronia_Paraburkholderia, Brevundimonas, Vibrio and Pseudomonas increased significantly (p<0.05). The analysis of the functional characteristics of the microbial communities reveals that the paths related to the Renin-angiotensin system, protein digestion, and Vibrio cholerae infection in diseased sea urchins increased significantly, while the Folate biosynthesis pathway decreased significantly (p<0.05). The results indicate that the microbial ecological balance and stability were reduced by red spot disease in the gut bacterial community of S. intermedius.