Bowel health is an important factor for duck rearing that has been linked to feed uptake and growth and death rates. Because the regulatory networks associated with acute stress-mediated injury in the duck gastrointestinal tract have not clearly elucidated, we aimed to explore potential miRNA-mRNA pairs and their regulatory roles in oxidative stress injury caused by transport stress. Here, 1-day-old mallard ducklings from the same breeder flock were collected and transported for 8 h, whereas the control group was not being transported. Various parameters reflecting oxidative stress and the tissue appearance of the intestine were assessed. The data showed that the plasma T-AOC and SOD concentrations were decreased in the transported ducklings. The intestine of the transported ducklings also displayed significant damage. High-throughput sequencing of the intestine revealed 44 differentially expressed miRNAs and 75 differentially expressed genes, which constituted 344 miRNA-mRNA pairs. KEGG pathway analysis revealed that the metabolic, FoxO signaling, influenza A and TGF-β signaling pathways were mainly involved in the mechanism underlying the induction of intestinal damage induced by simulated transport stress in ducks. A miRNA-mRNA pair, miR-217-5p/CHRDL1, was selected to validate the miRNA-mRNA negative relationship, and the results showed that miR-217-5p could influence CHRDL1 expression. This study provides new useful information for future research on the regulatory network associated with mucosal damage in the duck intestine.