Background: Pulmonary hypertensive crisis (PHC) is a serious life-threatening complication in children with congenital heart disease (CHD) after surgery, with acute onset and high mortality. However, there is still no effective means to deal with this complication. Therefore, our department developed the left atrium and right ventricle duct bridging technique to treat children with PHC, and compare its effects with conventional methods of treatment to determine the best solution for dealing with this complication. Methods: A retrospective analysis of 41 children with CHD surgery and postoperative PHC in our hospital from January 2015 to December 2022 was performed. According to the rescue method, the group with conventional therapy combined with left atrium to right ventricle duct bridging treatment vs. simple conventional therapy were defined as group A and group B respectively, with 13 cases and 28 cases in each group. The success rate of rescue, the complication rate, the length of intensive care unit stay, the delayed chest closure duration, the duration of PHC, the ratio of pulmonary circulation/systemic circulation pressure, the oxygenation index and the cardiac index at 30 min, 1 h, 2 h, 4 h and 6 h after rescue were compared between the two groups. Results: There was a higher success rate of rescue (84.62% vs. 68.86%; p > 0.05), lower complication rate (15.38% vs. 21.43%; p > 0.05), shorter duration of PHC (6.77 ± 2.13 min vs. 13.07 ± 4.05 min; p = 0.000), shorter duration of delayed sternal closure (32.23 ± 5.46 h vs. 38.14 ± 8.61 h; p = 0.029) and shorter length of ICU stay (81.69 ± 8.31 h vs. 93.57 ± 16.84 h; p = 0.021) in group A; After the rescue, the pulmonary artery pressure and cardiopulmonary function recovery rate in group A were faster than those in group B. Conclusions: In conclusion, left atrial to right ventricular duct bridging therapy is more effective in the treatment of PHC after surgery for CHD.