To investigate the difference of the compositional and functional structures of the intestinal microflora between healthy and diseased Litopenaeus vannamei, we screened the intestinal bio-indicators to evaluate the health status of the host, and assess the functional redundancy of the intestinal microflora in response to disease. Based on the Illumina high-throughput sequencing technology, we compared the intestinal microflora between healthy and diseased L. vannamei, and analyzed the functional profiles through the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). In addition, we estimated the correlation between the intestinal microflora structures and predicted the functional compositions. The results showed that the occurrence of disease was associated with significant changes of the bacterial community structures and functional compositions, and there was no significant change in bacterial diversity. Compared with the intestinal microflora of the healthy L. vannamei, the relative abundances of Actinobacteria, Planctomycetes and Verrucomicrobia significantly decreased in the diseased L. vannamei, whereas, the Gammaproteobacteria and Bacteroidetes exhibited an opposite pattern. In addition, 16 sensitive indicator families were screened, and their occurrences can indicate the health status of the host very well. Furthermore, the abundance of pathways involved in Vibrio spp. infection significantly increased in the diseased L. vannamei; in contrast, the pathways for antibacterial and immunity, such as lysosome and peroxisome pathways, markedly decreased in diseased shrimp. Notably, there was a significant and positive association in compositional and functional composition between the gut microbiota community, indicating a low functional redundancy of the shrimp gut bacterial community. The occurrence of disease was associated with the change of the intestinal microflora, which subsequently disrupts the bacterial-mediated functions. Further, this study provides sensitive bio-indicators for evaluating the host health status.