Crohn’s disease (CD) is a chronic inflammatory disease of the gastrointestinal tract arising in individuals with genetic predisposing factors and abnormalities of the immune system. Myelodysplastic syndrome (MDS), an acquired clonal hematologic disorder, is characterized by peripheral blood cytopenia, dysplastic changes in several types of hematopoietic cells of the bone marrow and peripheral blood, and a high risk of transformation to acute leukemia. CD rarely occurs in combination with MDS, and MDS treatment with hematopoietic stem cell transplantation (HSCT) has not been frequently reported. We report the case of a 50-year-old Chinese male who presented with abdominal pain, diarrhea, and fatigue. CD was diagnosed by colonoscopy, imaging studies, and pathological examination. He was initially treated with mesalazine and prednisone and thereafter he presented with pancytopenia. MDS (RAEB-I) was diagnosed by bone marrow examination, and karyotyping revealed 47, XY, +8. The patient was treated with thalidomide, andriol, and decitabine. Allogeneic HSCT was performed with a human leukocyte antigen-matched sibling as the donor. The patient is currently well at 14 months after HSCT, without abdominal pain, diarrhea, or fatigue. HSCT may be a promising treatment option for patients with combined CD and MDS.