The complex of oat β-glucan (OBG) and flavonoids hampered the digestion of starch-based food and retarded the blood glucose response; however, its effect on gastric emptying and its relative mechanism have not been thoroughly investigated. By using Fourier transform infrared (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), antioxidant ability, and enzymic inhibitory tests for the characterization and in vitro semi-dynamic digestion of complexes of OBG (high and low molecular weights) and sea buckthorn flavonoids, we found that the higher molecular weight complex (FU) exhibited stronger ABTS and DPPH radical scavenging abilities and higher α-glucosidase and α-amylase inhibition rates. Mice fed with rice flour with FU addition exhibited the slowest gastric emptying and intestinal propulsion rates and blood glucose rise and had the lowest activity of digestive enzymes and levels of insulin, ghrelin, motilin (MTL), and relevant gene (ghrelin and GHSR mRNA) expression than those in the control and low-molecular-weight groups. This study provided scientific data for the development of foods with delayed gastric rate and hypoglycemic index for specific populations.