Microcystis aeruginosa is a primary species of toxin-producing cyanobacteria. This study explored the effects of short-term exposure (96 h) to M. aeruginosa on the intestinal microflora variation and immune function of zebrafish. After exposure to different cell concentrations of M. aeruginosa, marked histological variation was observed in the intestine, such as goblet cells proliferation and intestinal desquamation. In addition high-concentration M. aeruginosa treatment (initial concentration: 1.59 × 105 cells mL−1) induced a significant increase in cytokine levels compared with other groups. Low-concentration M. aeruginosa treatment (initial concentration: 0.88 × 105 cells mL−1) promoted the transcription of inflammatory genes, while high-concentration treatment restrained the transcription of these genes. Moreover, M. aeruginosa exposure also changed the intestinal microbial diversity. At the phylum level, bacteria belonging to Proteobacteria were the most abundant in all groups, and Gammaproteobacteria were the dominant bacteria with major changes. Pathogenic microorganisms such as Shewanella, Plesiomonas, Halomonas, Pseudomonas, and Lactobacillus increased greatly after treatment with different cell concentrations of M. aeruginosa. This study indicates that M. aeruginosa induces an increase in zebrafish goblet cells and enhances the inflammatory response, which may produce detrimental effects in zebrafish, resulting in a greater proportion of pathogenic bacteria and intestinal injury. The results of this study will help improve the understanding of the effects of M. aeruginosa on the intestines of aquatic organisms.