The complete resection is one of the most crucial requirements to achieve favorable outcomes in oncologic surgery. The apex of the lung is surrounded complicatedly by the clavicle, the first rib, the subclavian artery and vein, and the brachial plexus. Therefore, the image information especially about the infiltration of adjacent anatomic structures, facilitates the surgery in the apical lung cancer. A 70-year-old man presented at our hospital with a computed tomography (CT) scan showing a tumor at the left lung apex that infiltrated the chest wall. Two anatomical anomalies were found, which were the first rib hypoplasia and the aberrant pulmonary artery branch. The three-dimensional (3D) CT enhanced with using bolus tracking method, simultaneously revealed that the subclavian vessels existed between the clavicle and the second rib, and the left lingual pulmonary artery and the ventrobasal pulmonary artery diverged from the left main pulmonary artery as the first branch. We diagnosed the tumor as a primary lung squamous cell carcinoma that infiltrated the second rib, because sputum cytology suggested squamous cell carcinoma. Left lung upper lobectomy with lymph node dissection and chest wall resection (the second and third ribs) were performed with caution for the anatomical anomalies. The pathological diagnosis was pleomorphic carcinoma (5.0?×?3.0?×?1.9 cm) that invaded the second costal bone, and the pathological stage was confirmed to be pT3N0M0. Pathologically curative resection was accomplished. The patient was discharged from the hospital on 10 days after surgery. The 3D-CT precisely detected the anomalous structure consisted with the clavicle, the second rib, the subclavian artery and vein, the aberrant pulmonary artery branch. In the present case with the apical lung cancer, the evaluation of the anatomical structure via 3D-CT facilitated to achieve a pathological complete resection.