Background: Intestinal ischemia–reperfusion injury (IIRI) is driven by oxidative stress, excessive inflammation, Endoplasmic Reticulum Stress (ERS), and disruption of the intestinal epithelial barrier. Corilagin, a natural ellagitannin with antioxidant and anti-inflammatory activities, has shown protective effects against IIRI; however, its cross-species and multitarget mechanisms remain unclear. Methods: This study investigated the protective mechanisms of Corilagin against IIRI by integrating Corilagin-related targets, IIRI-associated genes, and an ERS gene set. Differential expression analyses of GSE37013 and GSE96733 were combined with an ensemble machine-learning framework comprising 15 algorithms to prioritize core genes. Molecular docking and 100-ns all-atom molecular dynamics simulations using the AlphaFold-predicted full-length human NRF2 structure were performed to assess the predicted Corilagin-NRF2 interaction. A mouse IIRI model was used to validate selected molecular and histological findings by histology, RT-qPCR, Western blotting, and immunohistochemistry. In IEC-6 cells subjected to OGD/R, NRF2 immunofluorescence and siRNA-mediated knockdown of Nrf2 or Abcg2 were used to further evaluate the involvement of NRF2 and ABCG2 in Corilagin-mediated protection. Results: Intersection analysis identified 472 genes shared among Corilagin-related targets, IIRI-related genes, and ERS-associated genes. Enrichment analysis highlighted stress- and injury-related pathways, including PI3K-Akt signaling. Ensemble machine learning prioritized 12 core genes across human and mouse datasets, with ABCG2, IL10, and PRKCZ emerging as prominent candidates. Docking and 100-ns MD simulations supported persistent Corilagin retention within the predicted NRF2 binding region, while post-relaxation MM/GBSA analysis indicated favorable interaction energetics. In vivo , Corilagin pretreatment reduced inflammation and oxidative stress-related changes, restored apical ABCG2 and tight-junction protein expression, improved mucosal morphology, and altered CHOP expression. In IEC-6 cells, Nrf2 or Abcg2 knockdown weakened Corilagin-mediated preservation of Occludin, Claudin-1, and ZO-1 under OGD/R, supporting NRF2–ABCG2 involvement in this protective response. Conclusion: Corilagin may alleviate IIRI by modulating ERS-related molecular changes and preserving the intestinal epithelial barrier with NRF2 and ABCG2 contributing to a candidate regulatory module involved in this protective response. These findings provide computational and experimental support for further investigation of Corilagin as a potential intervention for IIRI and illustrate the value of combining multi-source data integration with ensemble machine learning to characterize the multitarget pharmacology of natural products.