Objective: The purpose of this article is to evaluate the efficacy of thoracoscopy assisted minimally surgery (NUSS procedure) for pectus excavatum and novel modified NUSS procedure by comparing the data of patients of pectus excavatum who had undergone novel modified NUSS Procedure or NUSS procedure. Methods: A retrospective study was performed, involving 132 cases of patients with pectus excavatum collected from Shanghai Jiaotong University School of Medicine Xinhua Hospital cardio-thoracic surgery between Jan. 2009 and Jan. 2012. The 132 patients were strictly divided into two groups: Group A included 76 cases that underwent a novel modified NUSS procedure; Group B included 56 cases that underwent NUSS procedure. Compared data included gender, age, operative time, blood loss, postoperative hospital staying and clinical variables and demographic were compared with univariable analysis. Results: No statistically significant correlations were observed in the two groups, such as age (12.67±4.793 years vs. 12.20± 6.423 years), sex, and other clinical data (P > 0.05). In Group A, postoperative hospitalization time (3.95±0.487 days vs. 6.07±1.412 days), operation time (46.28±12.218 minutes vs. 72.23±24.270 minutes), and blood loss (7.37±4.863 ml vs. 16.93±14.002 ml) were significantly better than those in Group B (P < 0.05), shortening hospitalization time, reducing costs, meaning statistically significant differences. There was no recurrence in Group A and Group B after operation. Conclusion: The study demonstrated that novel modified NUSS procedure is less invasive, having rapid recovery, shortening the time of hospital stay, and reducing hospital cost. Thus, it is safe, worth promoting, and is widely being used.