Objective To compare the short-term efficacy and long-term survival of patients with non-small cell lung cancer (NSCLC) treated by uniportal or three portal thoracoscopic radical resection. Methods A total of 388 patients who underwent uniportal or three portal thoracoscopic radical resection of lung cancer in the Department of Thoracic Surgery of Anhui Chest Hospital from 2015 to 2016 were analyzed retrospectively. The patients were divided into two groups including an uniportal group and a three portal group according to the procedure. The clinicopathological features, perioperative data and long-term survival of the two groups were compared. Results Finally, we included 205 patients with 105 males and 100 females at an average age of 58.73±10.93 years. There were 102 patients in the uniportal group and 103 patients in the three portal group. There was no statistical difference in clinicopathological features between the two groups (P>0.05). But compared with the three portal group, the uniportal group had less postoperative drainage, shorter postoperative catheterization time and postoperative hospital stay (P<0.05). There was no statistical difference in the number of lymph node dissection stations between the two groups (P=0.058). The pain score at 24 hours after operation in the uniportal group was significantly lower than that in the three portal group (P<0.001). There was no statistical difference in the total incidence of complications and the incidence of pulmonary complications between the two groups (P=0.161 and P=0.275). The median survival period and the 1st, 3rd, and 5th year survival rate in the uniportal group was 63.0 months and 95.0%, 75.2%, 51.5%, respectively. The median survival period and the 1st, 3rd, and 5th year survival rate in the three portal group was 61.0 months and 89.3%, 70.9%, 50.5%, respectively. There was no satistical difference in the survival results between the two groups (P=0.440). Conclusion Uniportal thoracoscopic radical resection of lung cancer is more minimally invasive and safe and effective in the treatment of NSCLC. It can make patients recover faster after operation.