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To investigate the characteristics of the intestinal flora of Exopalaemon carinicaudainfected with Enterocytozoon hepatopenaei (EHP), we analyzed the intestinal flora of the infested individuals by sequencing 16s rRNA genes. In this study, we analyzed the differences in species and abundance of intestinal flora in different EHP load groups (no load group (control group, C), high load group (H) and low load group (L)). The results showed that the intestinal flora diversity in group H was significantly lower than that of shrimp in group C (P < 0.05). UPGMA-based clustering tree and PCoA analysis showed that, unlike group C, bacterial communities clustered together in groups H and L, suggesting that infection with EHP could alter the compositional structure of shrimp gut microbes. By species abundance clustering heat map analysis, most of the dominant bacteria in groups L and C were beneficial bacteria, such as Lactococcus , Ligilactobacillus and Bifidobacterium。In contrast, most of the dominant genus in group H were pathogenic bacteria, such as Pseudomonas , Photobacterium andCandidatus_Hepatincola. By predicting the functions associated with intestinal flora, the genes associated with metabolism were more abundant in group C, metabolism and nervous system in group L, and disease and environmental processing in group H. This study provides an aid for further screening of EHP antagonist bacteria.