Pulmonary atresia with intact ventricular septum and critical pulmonary stenosis usually have to undergo treatment in the neonatal period. Compared to traditional surgical intervention, catheter-based cardiac interventions may achieve similar or superior outcomes for neonates with pulmonary atresia with intact ventricular septum and critical pulmonary stenosis. However, there is limited literature on anaesthesia techniques, challenges, and risks associated with cardiac catheterisation in this population. This article retrospectively analysed the clinical data of pulmonary atresia with intact ventricular septum and critical pulmonary stenosis neonates who were treated with interventional cardiac catheterisation in our hospital from January 2015 to October 2022. Clinical outcomes considered were haemodynamic or pulse oxygen saturation instability, vasoactive requirements, prolonged intubation (>24 h postoperatively), and cardiovascular adverse events. A total of 63 patients met the inclusion criteria. All patients survived the intervention. Among the patients with critical pulmonary stenosis, 40 successfully received percutaneous balloon pulmonary valvuloplasty, while three patients received ductal stenting due to moderate right ventricular dysplasia at the same time. For patients with pulmonary atresia with intact ventricular septum, 17 of the 23 patients successfully underwent percutaneous pulmonary valve perforation and percutaneous balloon pulmonary valvuloplasty. Of these, five patients underwent ductal stenting due to unstable pulmonary blood flow. Three patients only underwent ductal stenting. In addition, three patients received hybrid therapy. There are various clinical techniques and risk challenges in the interventional cardiac catheterisation of neonatal pulmonary atresia with intact ventricular septum and critical pulmonary stenosis. However, by mastering the physiological and pathophysiological characteristics of the disease, adequately preparing for the perioperative period, and predicting the procedure process and potential complications, anaesthesia and surgical risks can be effectively managed.