INTRODUCTION: Portal venous system thrombosis accompanied by intestinal infarction is a rare complication following blunt abdominal trauma. It is known to be caused by liver cirrhosis. Herein, we describe the clinical manifestations and treatment of portal venous system thrombosis in a patient, confirmed by imaging and pathology. CASE PRESENTATION: A 38-year-old Chinese woman presented with abdominal pain and vomiting after a car accident. Portal venous system thrombosis without other thrombophilic states was diagnosed via computed tomography angiography after 2 months. The patient developed small bowel infarction and received successful treatment via anticoagulation and surgery. CONCLUSION: This report demonstrates that vascular injury, including both hemorrhage and ischemia, should be considered in the differential diagnosis after abdominal trauma. Clinicians should be aware of portal venous system thrombosis following acute abdomen, especially when clinical presentations do not correspond to common situations. Early anticoagulation therapy can improve prognosis once the diagnosis is established.