Hereditary protein S deficiency (PSD) is an autosomal dominant disorder caused by mutations in the PROS1 gene which can cause venous thrombosis. Individuals with PSD usually present with recurrent deep vein thrombosis and/or pulmonary embolism, but thrombosis may occur at unusual sites, such as the mesenteric and portal veins. Here we report a case of hereditary protein S deficiency patient with predominant mesenteric venous thrombosis. A 57-year-old man was admitted for abdominal pain and bilateral lower limber swelling. His sister had a history of thrombotic disease. On admission, His temperature was 37.4 ℃, the pulse was regular, and the blood pressure was 130/79 mmHg. Abdominal examination showed right lower abdomen tenderness, rebound tenderness and suspected muscle rigidity. Abdominal computed tomography (CT) angiography found that the patient had superior mesenteric venous thrombosis (MVT) and perforation of intestine. Vascular ultrasound of lower limb indicated bilateral deep venous thrombosis. Although treatment of fasting, water restriction, parenteral nutrition solution, acid suppression, anti-biotic treatment and low molecular weight heparin for anticoagulation were given, abdominal pain were not relieved. Small intestine resection and anastomosis was done after. Pathology of intestine did not show changes indicative of vasculitis. To investigate the cause of multiple thrombosis, a work-up for hypercoagulability (protein C and S activities, antithrombin, lupus anticoagulant, anti-cardiolipin antibody, anti-β2 glycoprotein Ⅰ antibody) was done and the result showed increased dRVVT ratio and the significantly decreased protein S levels. Anti-phospholipid syndrome (APS) was suspected because of the thrombosis and positive lupus anticoagulant, but at the time of the test the patient was on oral anticoagulants which might influence the result of lupus anticoagulant. The lupus anticoagulant was normal after discontinuing oral anticoagulants and APS was excluded. Because of his personal and family history of thrombotic disease, a hereditary thrombophilia was suspected and a laboratory analysis showed a reduced protein S activity. Further examination of the whole exome sequencing indicated a heterozygous mutation in the PROS1 gene. He was diagnosed with hereditary protein S deficiency and was started on anticoagulant therapy with rivaroxaban. He had been followed up for 1 year, and his condition kept stable without newly developed thrombosis or bleeding.