Objective To explore the feasibility and efficacy in therapy of pectus excavatum using novel modified Nuss procedure after congenital heart disease (CHD) operation. Methods Thirty-six children (including 22 males and 14 females with an average age of 4.5±2.2 years ranging 2.8-18.0 years) with pectus excavatum after CHD operation from January 2011 to March 2015 were selected as an observation group. Thirty-eight pectus excavatum children (including 24 males and 14 females with an average age of 4.0±2.5 years ranging 2.8-20.0 years) without CHD from July to September 2013 were selected as a control group. The novel modified Nuss procedure was performed on the patients in both groups. The operation time, intraoperative blood loss, hospital stay as well as postoperative complications between two groups were reviewed and analyzed. Results In the observation group, the operation time was 50-72 (60.50±3.60) min and hospital stay was 4-6 (4.41±0.80) d. Meanwhile, the intraoperative blood loss was 5-10 (5.82±0.35) ml. In the control group, the operation time was 12-45 (20.15±0.68) min, hospital stay was 4-7 (4.61±0.63) d and the intraoperative blood loss was 3-8 (4.62±0.28) ml. The operation time was significantly longer in the observation group than that in the control group (P<0.05). But there was no significant difference in intraoperative blood loss or hospital stay between the two groups (P>0.05). No cardiac rupture happened in the two groups. Conclusion The novel modified Nuss procedure is safe and feasible for pectus excavatum after CHD operation with optimal outcomes.