Emerging evidence shows that dietary oligosaccharides are important prebiotics that can improve intestinal flora, while dietary polyphenols can act directly on intestinal cells. However, information about their synergistic effects on gut health is still limited. In this study, alginate oligosaccharide (AOS) and cyanidin-3-O-glucoside (C3G) were selected as a common marine plant oligosaccharide and terrestrial plant polyphenol, respectively, to study their effects on intestinal health. The results show that, in comparison to their individual applications, the combination of AOS and C3G (mass ratio, 3:1) displayed a stronger ability to up-regulate the expression of tight junction proteins, while enhanced intestinal epithelial barrier was also observed and levels of mucin-2 and β-defensins were simultaneously increased in the intestinal mucus. Interestingly, the secretion of immunoglobulin A and immune-related cytokines were approximately doubled by the AOS + C3G mixture. In addition, the AOS + C3G mixture was found to be more conducive to the positive transformation of intestinal flora, which stimulated the growth of beneficial bacteria Akkermansia, Lachnospiraceae and Feacalibaculum while inhibiting the growth of harmful bacteria Helicobacter and Turicibacter. The data generated herein thus suggests that dietary oligosaccharides and dietary polyphenols may be more beneficial to intestinal health when applied in combination than their individual effects alone.