Objective To explore the factors influencing the duration of mechanical ventilation after surgery in children with congenital heart disease (CHD). Methods The clinical data of children with CHD aged≤6 months who received surgical treatment at the Pediatric Heart Center of the hospital from October 2020 to December 2023 were retrospectively analyzed. Based on the duration of mechanical ventilation, the patients were divided into a prolonged mechanical ventilation group (≥72 hours) and a control group (<72 hours). Clinical characteristics between the two groups were compared, and the factors influencing the occurrence of prolonged mechanical ventilation after CHD surgery were analyzed. Results A total of 119 children (64 boys and 55 girls) with CHD who received surgery were included and the median age was 47.0 (17.0-81.0) days. There were 54 (45.4 %) children with undernutrition (WAZ<-1). Among them, 33 children had WAZ<-2. There were 29 patients in the prolonged mechanical ventilation group and 90 patients in the control group. Multivariate logistic regression analysis showed that undernutrition and increased risk adjustment for congenital heart surgery-1 (RACHS-1) score were independent risk factors for predicting prolonged mechanical ventilation (P<0.05), and elevated serum albumin was an independent protective factor for predicting prolonged mechanical ventilation (P<0.05). All CHD children recovered and were discharged after treatment. Conclusions In children undergoing surgery for CHD, prolonged mechanical ventilation after surgery should be monitored in patients with preoperative malnutrition, hypoalbuminemia, and high RACHS-1 scores.