Pulmonary embolism is a disease difficult to diagnosis and management with high mortality. Incidence rate was low in complications of cancer surgery. We reported a patient with oral cancer who underwent wide excision, bilateral selective neck dissection and free flap reconstruction. Nine days after surgery, we found rapid shallow breathing, low SpO_2 of the patient. Arterial blood gas analysis showed hypoxemia. Blood tests showed a D-dimer level higher than normal. Echocardiography revealed normal left ventricular function, right ventricular dilatation, pulmonary hypertension and severe tricuspid reflux. Chest computed tomography showed bilateral pulmonary embolisms. The bilateral pulmonary emboli were surgically removed under the use of cardiopulmonary bypass. The aim of this article was by this case we can know the diagnosis, treatment and prevention of pulmonary embolism after head and neck surgery.