The biological activity of mangosteen peel proanthocyanidin extracts is related to digestive properties and colonic metabolism. Therefore, the study's aim was to investigate the dynamics of proanthocyanidin extracts during in vitro digestion and colonic fermentation, their protective effects against oxidative damage in PEC-J2 cells, and their interactions with the intestinal flora. The results showed that epicatechin and proanthocyanidin B2 were the most abundant in proanthocyanidin. In addition, the catechin was increased by 27.7 ± 0.2 μg/mL. The total phenol content, total flavonoid content, and proanthocyanidin content of mangosteen peel were reduced by 32.36%, 90.63%, and 78.06%, respectively. However, the antioxidant capacity was increased by two-fold, protecting against oxidative damage in cells. Proanthocyanidin polymers that are not digested by the gastrointestinal tract go to the colon, where they are metabolized by microorganisms to produce short-chain fatty acids (SCFAs). Proanthocyanidin extracts modulated the microbial flora structure: the relative abundance of Phascolarctobacterium, Roseburia, Faecalibacterium, Coprococcu, and Clostridium sensu stricto all increased significantly. The ratio of Bacteroides to Firmicutes increased, and Bifidobacterium grew and multiplied. This study improves the utilization of mangosteen peel and provides a theoretical basis for the scientific evaluation of the antioxidant activity and gut microbiota modulation of mangosteen peel.