Abstract: The grass carp (Ctenopharyngodon idellus) infected with the hemorrhage virus was used to analyze the intestinal microbiota by using high-throughput sequencing. The results showed that microbiota significantly differed between grass carp reovirus (GCRV)-infected and control grass carp (multiple response permutation procedure (MRPP), analysis of similarity (Anosim), and Adonis; P<0.01). When we compared alpha diversity, we found that Shannon-Wiener index, inverse of Simpson's original index and Pielou’s evenness index of intestinal microbiota were all significantly decreased after infecting with GCRV (independent samplest-test, P<0.05). Besides, we found that the individual difference within GCRV-infected group was significantly greater than those in the controls (Wilcoxon signed-rank test,P<0.05), suggesting that the intestinal microbiota in GCRV-infected grass carps became disorganized and lost their original balance. Proteobacteria, Firmicutes, Fusobacteriaceae, and Bacteroidetes were dominant phylum in both GCRV-infected group and controls. However, the relative abundance of operational taxonomic units (OTUs) between the two groups was different. For example, OTU_69 (Pasteurellaceae), OTU_504 (Comamonadaceae), and OTU_1898 (Cetobacterium) were all significantly lower than that of controls (t-test, P<0.05), confirming that GCRV could make intestinal microbiota of grass carps disorganized. The stability of intestinal microbiota is important for health of host. By detecting changes in the intestinal microbiota of GCRV-infected grass carp, we will be able to provide theoretical basis and data reference for the prevention and treatment of common disease of farmed fish, as well as providing a reference for healthy breeding.