Biological treatment by black soldier fly larvae (BSFL) has proven to be an effective method for the resource utilization of cyanobacteria, but the effects of microcystin-LR (MC-LR) in cyanobacteria on BSFL growth have not been adequately explored. To evaluate the inhibitory effect and toxic mechanism of MC-LR on BSFL, the growth performance and intestinal microbiota were examined after exposure to 0, 10, 100, and 1000 mu g/kg of MC-LR. The larval weight and survival rate were each significantly inhibited by 21.53% and 21.49% compared with the control group, respectively, after exposure at a concentration of 1000 mu g/kg MC-LR for 16 days. Lipid accumulation, intestinal inflammation, and oxidative stress were observed in three treatment groups, with dose-dependent inflammation ocurring in the intestine. Compared with the control group, superoxide dismutase and catalase activity levels were significantly increased by 74.91% and 49.58%, respectively, which confirmed the occurrence of oxidative stress induced by MC-LR. Furthermore, MC-LR altered the diversity of intestinal microbiota and increased the relative abundance of pathogenic bacteria (e.g., Paenibacillus, Clostridium_sensu_stricto_1, and Lachnoclostridium), which increased the risk of disease in BSFL and contributed to observed metabolic disorders. On the other hand, qRT-PCR analysis further confirmed the occurrence of oxidative stress and the activation of the peroxisome proliferator-activated receptor signaling pathway, resulting in the upregulation of fatty acid synthesis-related genes, ultimately leading to lipid accumulation and apoptosis. These findings provide valuable insights into the ecological risks associated with MC-LR during the process of cyanobacterial resource utilization.