Objective To explore the treatment method of congenital heart disease (CHD) with pulmonary artery hypertension (PAH) in infants with Down syndrome (DS). Methods The clinical data of 60 CHD patients with PAH from March 2015 to August 2016 in our hospital were retrospectively analyzed. There were 30 infants with DS classified as a DS group (trial group, 17 males and 13 females with a mean age of 1.15±0.25 years) and the other 30 patients without DS were classified as a control group (20 males and 10 females with a mean age of 1.24±0.30 years). All the patients underwent surgical treatment and fasudil combined with sildenafil were used to prevent pulmonary hypertension crisis postoperatively. Results There was no significant difference in cardiopulmonary bypass time, aortic cross-clamping time, modified ultrafiltration time and the incidence of postoperative respiratory complications between the two groups. The pulmonary systolic blood pressure significantly decreased at 24 h after operation in the two groups (both P<0.05). The arterial oxygen pressure and oxygenation index of the trial group were lower than those of the control group at 6 h after operation (both P<0.05). The mechanical ventilation time and intensive care time of the trial group were significantly longer than those of the control group (P=0.007 and P=0.000, respectively). There were no reoperations or early death. Conclusion The effects of surgical repair of CHD with PAH in infants with DS are satisfactory by grasping the indication, protecting lung function and controlling PAH in the early postoperative period, although there is a high incidence of pulmonary complications.