Chlorogenic acid (CGA) and epigallocatechin-3-gallate (EGCG) are major polyphenolic constituents of coffee and green tea with beneficial health properties. In this study, we evaluated the gut protecting effect of CGA and EGCG, alone or in combination, on D-galactose-induced aging mice. CGA plus EGCG more effectively improved the cognition deficits and protected the gut barrier function, compared with the agents alone. Specifically, CGA plus EGCG prevented the D-galactose mediated reactive oxygen species accumulation by increasing the total antioxidant capacity, reducing the levels of malondialdehyde, and suppressing the activity of the antioxidant enzymes superoxide dismutase and catalase. In addition, supplementation of CGA and EGCG suppressed gut inflammation by reducing the levels of the proinflammatory cytokines TNFα, IFNγ, IL-1β and IL-6. Moreover, CGA and EGCG modulated the gut microbiome altered by D-galactose. For instance, CGA plus EGCG restored the Firmicutes/Bacteroidetes ratio of the aging mice to control levels. Furthermore, CGA plus EGCG decreased the abundance of Lactobacillaceae, Erysipelotrichaceae, and Deferribacteraceae, while increased the abundance of Lachnospiraceae, Muribaculaceae, and Rikenellaceae, at the family level. In conclusion, CGA in combination with EGCG ameliorated the gut alterations induced by aging, in part, through antioxidant and anti-inflammatory effects, along with its gut microbiota modulatory capacity.