Graft-versus-host disease (GVHD) and infection are the frequently encountered complications after hematopoietic stem cell transplantation (HSCT), which influence the outcome and limit the widespread application of HSCT. Intestinal microbiota plays an important role in maintaining intestinal immune balance. The diverse levels of intestinal microbiota associated with the incidences of GVHD, infection and the prognosis of HSCT, thus remodeling intestinal microbiota can alleviate GVHD and infection after HSCT. Herein, the recent research progress about the role and the involved mechanisms of intestinal microbiota in HSCT, and the novel manipulation strategies of intestinal microbiota are systematically reviewed.