The early stage of shrimp aquaculture is susceptible to bacterial infection and the bacterial community structure in digestive tract is highly associated with shrimp health. Therefore, it is of great significance to explore the relation between shrimp bacterial community of digestive tract and juvenile shrimp disease. We investigated the intestinal bacterial community composition of healthy and diseased juvenile shrimp (Litopenaeus vannamei) by using Illumina sequencing, and explored Vibrio diverstiy based on 16S rDNA, recA and pyrH gene sequences of Vibrio isolates. The results showed that the average relative abundances of Alphaproteobacteria and Firmicutes are higher in healthy juvenile shrimp digestive tract than those in diseased one, while these of Gammaproteobacteria, Bacteridetes, Actinobacteria and Betaproteobacteria exhibited an opposite pattern and the variation in Actinobacteria is significant. In addition, response ratio analysis at the bacterial family level shows that the relative abundances of Planococcaceae and Bacteriovoracaceae families significantly decreased, while that of Vibrionaceae remarkably increased in diseased juvenile shrimp digestive tract in relation to healthy one. Similarity percentage (SIMPER) analysis revealed that the main contribution to the variation of intestinal bacterial community structure between healthy and diseased shrimp is attributed to 8 OTUs affiliated with Vibrio, unclassified Rhodobacteraceae, Marivita, Cryobacterium, unclassified Microbacteriaceae and Pseudoalteromonas. As to Vibrio assamblege composition, we found that culturable V. sinaloensis strains were the dominant species in healthy juvenile shrimp digestive tract, while V. campbellii is dominant in diseased juvenile shrimp.