Enterocytozoon hepatopenaei (EHP) is a highly infectious intracellular parasite that primarily parasitizes the hepatopancreas, intestine, and muscle of shrimp. It can reproduce by consuming ATP from the host cells, resulting in growth retardation or even growth cessation of the host and increasing individual differences within a population. In recent years, we discovered EHP infection in the breeding process of Exopalaemon carinicauda culture, which has caused losses to the E. carinicauda culture industry. Intestinal microorganisms, which play a very important role in the growth and development of shrimp, can regulate nutritional metabolism, resist pathogen infection, and also have an important impact on the host immune function. Therefore, it is helpful to clarify the pathogenesis of EHP by exploring the differences and functions of the intestinal microflora between healthy and diseased shrimp. To screen potential probiotics for inhibiting or slowing down the spread of EHP, this study analyzed the intestinal microflora structure of shrimp based on 16s rRNA gene sequencing, and further explored the effect of EHP infection on the intestinal microflora of E. carinicauda. The results showed that the intestinal microflora of infected shrimp was significantly different from that of healthy individuals, and the structural diversity of the intestinal microflora was significantly lower than that of the healthy shrimp. Proteobacteria, including Desulfovibrionaceae, Vibrionaceae, unidentified Cyanobacteria, Mycoplasmataceae, and unidentified Alphaproteobacteria were the dominant bacteria in diseased shrimp, whereas Firmicutes including Lactobacillaceae, Bifidobacteria, Bacillaceae, and Chitinophagaceae were dominant in healthy shrimp. Infection with EHP significantly increased the potential pathogenic bacteria level in the intestines of the infected shrimp (P<0.05), and increased their susceptibility to other diseases. In addition, through the Tax4Fun function prediction, we found that the primary function of the intestinal microflora in infected shrimp was metabolism to resist EHP infection, whereas the intestinal microflora of healthy shrimp was primarily involved in individual growth and environmental information processing to ensure growth and survival.