A variety of disease in the chest can be treated with thoracoscopic surgery. Although with limited experience, thoracoscopic surgery can be performed with single-port approach. Theoretically, single-port approach can be applied in treating bilateral pleural effusions. Here we reported a case of 28-year-old man with the diagnosis of septic embolization of the lung with complications of bilateral empyema. He was treated with single-port thoracoscopic surgery for decortication of right pleural space and deloculation of left pleural space. After prolonged course of antibiotics for 21 days, the patient was discharged. After follow-up for 3 months, the patient recovered well and had no evidence of recurrence.