Given that lactoferrin (LF) exerts an excellent protection of intestinal homeostasis, the underlying mechanisms, especially epigenetic regulations, are still unknown. This study aimed to investigate the effects of dietary LF epigenetically modulates the oxidative genes by histone modifications to ameliorate ileum inflammation of mice exposed to DON contaminated diet. As expected, we found in the morphology analysis that DON exposure increased ileum crypt depth (CD) and villus width (VW) but reduced villus height (VH) and VH: CD ratio compared to those of the vehicle group. Consistently, the elevated ROS and MDA, along with the decreased ATP, SOD, CAT, GSH, and complex I, III, V were observed in the DON-exposed mice ileum. In contrast, LF markedly ameliorated the impairments of morphological and biochemical indexes. Next, we conducted transcriptome analysis to explore the changed signaling pathways using the ileum RNA of the mice treated with DON or LF. Firstly, the cell cycle pathway genes were significantly downregulated in the DON-exposed mice, and LF improved the cell cycle profile. Again, gene ontology analysis showed that inflammation and oxidative stress were significantly activated by DON exposure, and these were recovered when the DON-exposed mice were supplemented with an LF diet. Consistent with these findings, the signaling pathways of the reduced oxidative phosphorylation and elevated TNFα were also observed to be ameliorated by LF treatment. Importantly, histone modifications, including acetylation, methylation, and lactylation were suggested to be the vital players involved in the DON or LF treatment, in which LF significantly increased the loss of histone modifications on these genes. With a bioinformatics analysis and validation by qRT-PCR, the nuclear receptor NR5A2 was selected as a key master in the ileum of mice stimulated by DON. LF performed the benefit function on the NR5A2-mediated oxidative stress genes Ncoa4 and Prdx3 in the DON-exposed mice. Moreover, a ChIP-qPCR was used to verify that histone marks involving H3K9ac, H3K18ac, H3k27ac, H3K4me1, H3K9la, and H3K18la facilitated the epigenetic regulation of NR5A2-modulated actions. We conclude that dietary LF effectively ameliorated ileum lesions induced by DON in mice by modulating oxidative genes Ncoa4 and Prdx3 through histone modifications.