Oat protein is unstable in intestinal fluid digestion, and it is easily degraded by trypsin and chymotrypsin, producing low molecular weight peptides. Endopeptidase hydrolysis can improve the bioavailability of active peptides and avoid further digestion in the gastrointestinal tract. Antimicrobial peptides (AMPs) can effectively improve host immunity, but most related studies focus on physiology and ecology, and there are few reports on their molecular level. Therefore, in this article, oat peptides were prepared via the simulated digestion method in vitro, and the main metabolites and action factors affecting colitis were screened by using the multi-omics methods in a high-throughput mode to analyze the effect and mechanism of colitis. Firstly, oat antimicrobial peptides were prepared from cationic resin combined with HPLC, and the anti-inflammatory effects of antimicrobial peptides were analyzed in vitro through the use of human colon epithelial (HCoEpiC) anti-inflammatory cells. In vivo experiments using rats have verified that AMPs can effectively prevent colitis caused by dextran sodium sulfate (DSS), reduce intestinal inflammatory cell infiltration and glandular disappearance in the colon, and reduce the apoptosis rate of colon cells. Secondly, metabolomics and transcriptomics were combined to analyze the mechanism of preventing enteritis, and it was found that oat antimicrobial peptides can promote DAG diglycerol production and inhibit the activation of T helper cells (TH), resulting in the down-regulation of key factors in the main downstream pathways of TH1, TH2 and TH17, and inhibit the production of inflammatory cells. At the same time, AMP can activate the wnt pathway, improve the expression of key genes of wnt and frizzled, promote the generation of intestinal stem cells, facilitate the differentiation and repair of intestinal epithelial cells, and prevent the generation of enteritis. Finally, the underlying genetic regulatory network of the important pathway was constructed from the effect of AMP on rat colitis.