We report a case of pulmonary squamous cell carcinoma complicated with a tumor thrombus in the left atrium. The left atrial tumor thrombus, together with the left lower lobe, was removed via complete video-assisted thoracoscopic surgery (VATS), with cardiopulmonary bypass standby. The patient recovered well from surgery, received four cycles of postoperative chemotherapy, and is now under follow-up at the outpatient clinic. Although the optimal treatment is still controversial, simultaneous VATS and atriotomy under the premise of preoperative evaluation of the thrombus, including size and extent, might prevent systemic embolization and sudden death, alleviate the wound, promote postoperative rehabilitation, and improve prognosis in selected patients.