Background Hyperoxia treats a subset of critical neonatal illnesses but induces intestinal damage in neonatal pups. In this process, the intestinal flora and mucosal epithelium might be altered by hyperoxia. So the changes of the intestinal flora and mucosal epithelium were studied. Methods Neonatal rats were randomized into the model group that was exposed to hyperoxia and the control group that was maintained under normoxic conditions; then, intestinal lavage fluid and intestinal tissues were harvested. ELISA was used to detect D-lactic acid (D-LA), endotoxin (ET), diamine oxidase (DAO), intestinal fatty acid binding protein (i-FABP), liver-type fatty acid binding protein (L-FABP) and cytokines in the intestinal lavage of neonatal rats during hyperoxia. The intestinal zonula occluden-1 (ZO-1), occlusion protein (Occludin), and closure protein-4 (Claudin-4) of neonatal pups were detected by immunohistochemistry, western blotting, and real-time Polymerase chain reaction (RT-PCR) during hyperoxia. NCM460 cell survival rates were assayed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) during hyperoxia and administration of N-acetyl-L-cysteine (NAC). The expression levels of ZO-1, Occludin, and Claudin-4 in NCM460 cells were detected by immunohistochemistry, western blotting, and RT-PCR during hyperoxia and NAC. Results D-LA, ET, L-FABP, i-FABP, DAO, TNF-α, IL-10, and IFN-γ were significantly increased by hyperoxia, while ZO-1, Occludin, and Claudin-4 were clearly decreased in the hyperoxia group compared with the control group. NAC promoted cell survival, which was inhibited by hyperoxia. The cellular expression levels of ZO-1, Occludin, and Claudin-4, which were lowered by hyperoxia, were increased by NAC. Conclusion Hyperoxia causes injury of the intestinal mucosa, and ROS plays a role in this intestinal damage during hyperoxia.