Pyraclostrobin (PY) is highly toxic to aquatic organisms , and its increased residues in aquatic environments may have harmful effects on the intestine of aquatic creatures. Previous research demonstrated that vitamin E (VE) alleviated the acute toxicity of PY to zebrafish. This study further explored the mitigation effect of VE on PY-induced intestinal toxicity in fish and the underlying mechanisms by exposing adult zebrafish to PY (10, 20 μg/L) with or without 4 μM VE supplementation for 21 days. The results showed that VE alleviated the gut histopathological lesions caused by PY. VE co-exposure also improved PY-induced intestinal inflammation and restored the expression level of genes encoding intestinal tight junction protein . Furthermore, VE restored the anti-oxidation level inhibited by PY and reduced pro-apoptotic cytokine level and apoptotic enzyme activity increased by PY. 16S rRNA high-throughput sequencing showed that VE improved the zebrafish intestinal flora imbalance caused by 20 μg/L PY, increased the relative abundance of beneficial bacterium Cetobacterium , and reduced the relative abundance of pathogenic bacteria. In conclusion, VE alleviated PY-induced intestinal toxicity via repairing the damaged intestinal mucosal barrier , inhibiting inflammation, reducing oxidative stress and apoptosis, and improving the intestinal microbial disorder in zebrafish. • Vitamin E (VE) protected the intestinal barrier from damage of pyraclostrobin (PY). • VE inhibited intestinal inflammation induced by PY in zebrafish. • VE reduced oxidative stress and apoptosis levels in PY-exposed zebrafish. • VE improved the intestinal microbial disturbance in zebrafish caused by PY.