Venous thromboembolic disease is one of the common complications of hospitalized patients and is associated with high morbidity, high mortality and increased hospitalization costs. We reported the case of a 67-year-old male patient with a history of polycythemia vera (PV), who presented with abdominal distension, abdominal pain after improper diet. A contrast-enhanced computed tomography scan showed small bowel obstruction, perforation, appendicitis, and peritonitis. He were given non-operative treatmentincluding fasting, decompression tube placement, and anti-infection. The symptoms of ileus improved and the lesion was localized, but thrombosis was found in the subclavian vein, internal jugular vein, and upper limb vein on the left. Both of the sepsis and PV were thought to contribute to thrombosis. Heparin was used for anticoagulation and hydroxyurea for PV. Further laboratory tests revealed that serum antiphospholipid antibodies, anti-β2-glycoprotein Ⅰ antibodies and lupus anticoagulant were positive. With a combination therapy of anticoagulation, steroid, hydroxychloroquine and antibiotic, the patient's condition rapidly improved. Most venous thrombosis disappeared at half a year outpatient follow-up. Antiphospholipid syndrome (APS) and myeloproliferative neoplasms (MPN) are both associated with increased risk of thrombosis, but co-existence of these two conditions is rarely reported. Early diagnosis and treatment of thrombotic etiology are crucial to improve the course and prognosis of thrombosis.