Microcystis aeruginosa is a common kind of harmful bloom algae, which was also frequently found as a dominant microalgae specie in shrimp breeding ponds. And it was found that blooms always induced massive death of shrimp, but the toxic effects of M. aeruginosa on Litopenaeus vannamei are still not completely understood. In this paper, the toxicity of M. aeruginosa cells to L. vannamei was examined, and the toxic components in the cells were analyzed through high-pressure liquid chromatography (HLPC). In addition, the immune response of shrimp to the microalgal extract was assessed by measuring the activity of immune-related enzymes, as well as the transcription of the relevant genes. Overall, both M. aeruginosa cells and the algal extract resulted in a 100% mortality rate in shrimp, whereas the cell-free culture medium was ineffective. And HPLC analysis results revealed the presence of microcystin-LR (MC-LR) at a concentration of 190.40 mg/kg of cells. In addition, the activity and gene transcription of two immune related enzymes, SOD and LZM, were both significantly reduced in shrimp hepatopancreas (p<0.05) after injection with cell extract. However, reduced glutathione (GSH) content was slightly increased, but the ratio of GSH to GSSG was down, and the transcription of gst gene function as detoxification, was significantly downregulated (p<0.05). The results demonstrated that M. aeruginosa cell extract was highly toxic to L. vannamei, and exerted a negative effect on shrimp immunity including reduction of antioxidant capacity, antibacterial activity and detoxification activity, due to microcystin-LR.