Approximately 25% of global crops are estimated to be contaminated with one or more mycotoxins. The simultaneous exposure to deoxynivalenol (DON) and aflatoxin B1 (AFB1) poses a significant threat to human and animal health. To elucidate the toxicological mechanisms underlying their combined effects, we investigated the inflammation, intestinal barrier, endoplasmic reticulum (ER) stress, and apoptosis in both IPEC-J2 cells and C57BL/6 mice following treatment with DON and AFB1. Our findings demonstrated that combined exposure to these mycotoxins exacerbated inflammatory responses, impaired intestinal barrier integrity, triggered ER stress, and promoted apoptosis. These results indicated that the interaction between DON and AFB1 exerts a synergistic impact on driving these pathophysiological processes. This study underscores the necessity of accounting for mycotoxin cocontamination in the risk assessment of food and feed safety, and it offers valuable insights into the potential mechanisms driving the adverse health outcomes of mycotoxin exposure.