This study investigated the effects of dietary biogenic selenium nanoparticles (SeNPs) supplementation on oxidative stress-induced intestinal barrier dysfunction in mice. Selenium deficiency caused redox imbalance, inflammation, gut microbiota dysbiosis, and mitochondrial dysfunction, leading to intestinal barrier injury. SeNPs supplementation alleviated diquat-induced intestinal barrier dysfunction by enhancing antioxidant capacity, inhibiting ROS overproduction, protecting mitochondrial function, regulating immune response, and maintaining gut microbiota homeostasis via the Nrf2-mediated NLRP3 signaling pathway. Fecal microbiota transplantation further confirmed the role of SeNPs-modulated gut microbiota in protecting against intestinal dysfunction. Dietary SeNPs supplementation prevents oxidative stress-induced intestinal barrier dysfunction through mitochondria and gut microbiota regulation.