Mesenteric venous thrombosis (MVT) is a serious condition due to its potential association with mesenteric ischemia and infarction of the small bowel. Symptoms of MVT are often vague, making accurate diagnosis and sufficient treatment difficult. However, increased awareness and new imaging modalities for this condition have improved outcomes for patients with MVT. Treatment includes anticoagulation, transcatheter therapy, and surgery. In the present report, we describe the case study of a 62-year-old woman with a presenting diagnosis of superior MVT, who was finally diagnosed with myelodysplastic syndrome. The superior MVT spontaneously dissolved after the patient underwent 6 months of systemic anticoagulation therapy. Invasive surgery or bowel resection was not required.