Regeneration of epithelia is crucial for maintaining the intestinal barrier and homeostasis. Our previous work showed that exopolysaccharides from NCU116 (EPS116) regulated the barrier function and homeostasis of the intestine; however, the relevant mechanisms remain obscure. Therefore, we sought to explore the role of EPS116 in promoting intestinal epithelial regeneration. Our data showed that the administration of EPS116 markedly ameliorated inflammatory bowel disease-related phenotypes and promoted the regeneration of crypts in the colon of colitis mice. The results of immunofluorescence and reverse transcription-quantitative polymerase chain reaction experiments indicated that EPS116 strikingly increased the number of intestinal stem cells (ISCs) and the expression of differentiation markers for goblet cells, enterocytes, and enteroendocrine cells in the mouse colon. Intestinal microbiota analysis showed that EPS116 increased microbial populations associated with intestinal regeneration and glycan metabolism. Therefore, the present study revealed a novel model that EPS116 promoted the intestinal homeostasis through modulating the proliferation and differentiation of ISCs and altering the gut microbiota profile.