Early-life nutritional supplementation can dramatically influence health status. Dietary polyphenols are a widespread group of phytochemicals with potential bioactive functions. However, how polyphenol intake during early life affects health status remains largely unknown. Mice aged 3- and 6-weeks were used to investigate how grape polyphenol extract (GPE) administration during early life altered polyphenol absorption, the intestinal microbiota, and the intestinal barrier. After a 2-week GPE supplementation, there were more diverse polyphenol metabolites in the plasma of 3-week-old mice than in the plasma of 6-week-old mice. Correspondingly, GPE supplementation increased the mRNA expression of genes related to polyphenol absorption in 3-week-old mice but not 6-week-old mice. Early-life GPE administration also stimulated the key genes of the small intestinal barrier in mice. Moreover, the key genes of the small intestinal barrier were positively associated with the genes related to polyphenol absorption in the small intestine of 3-week-old mice. In addition, fecal Akkermansia and Lactobacillus were increased, as evidenced by 16S rRNA gene sequencing. As a result, the acetate and butyrate production in the large intestinal content was enhanced, and the mRNA expression of the key genes involved in the large intestinal barrier was also increased. Thus, our study demonstrates that dietary polyphenol intake in early life induces improvements in polyphenol absorption, the intestinal microbiota, and the intestinal barrier, suggesting the importance of polyphenol-rich nutritional programming during early life on health status.