Abstract: whole grain oat consists of bran, endosperm, and embryo, and different parts of oats consist of different nutrients that are closely related to human health. Therefore, there may be differences in the digestion products of peeled oat (PO) and whole grain oat (UO), leading to differences in nutritional properties. To investigate the effects of different nutrient composition on post-digestion metabolites as well as metabolic pathways, metabolites from the small intestinal sites of PO and UO were first collected after in vitro digestion. Then, the metabolites were determined using ultra performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS), and orthogonal projections to latent structures discriminant analysis (OPLS-DA) and cluster analysis were used to screen for the differences in metabolites. The results showed that 156 differential metabolites were identified by comparison with the HMDB database and screening of variable importance in projection (VIP) and P values. Among them, 63 were lipid and lipid-like molecules, 46 were organic acids and their derivatives, and 16 were phenylacetones and polyketides. In addition, the KEGG signaling pathway was searched and a greater enrichment was found for starch and sucrose metabolism, fructose and mannose metabolism, flavonoid biosynthesis, and biosynthesis effects of various plant secondary metabolites. It can be concluded that there are differences between the metabolic pathways of oats with different nutrient compositions after simulated digestion in the small intestine in vitro, which may have different health benefits.