Background: Transcatheter and intraoperative device closures have been widely used in the treatment of secundum atrial septal defect (ASD). However, for young infants with ASD, device closure remains controversial, and such treatment features limited data. We compared the clinical data and follow-up results of percutaneous and intraoperative device closure for ASD to evaluate the feasibility, safety, and efficacy of both treatments in infants under 3 years of age. Methods: From September 2010 to September 2018, 186 children under 3 years of age with significant secundum ASD were included in this study. A total of 88 and 98 patients were divided into groups A (transcatheter device closure) and B (intraoperative device closure), respectively. The clinical data and follow-up results of the two groups were analyzed retrospectively. Result: The mean age and weight of patients in group A were significantly higher than those in group B. The proportion of complex ASDs (multiples or rims deficiency) and the device/weight ratio in group B were significantly higher than those in group A. Successful closure was obtained in 86 (97.7%) and 96 (98.0%) infants in groups A and B, respectively, with two failed cases in each group (2.3% vs 2%). The rate of periprocedural complications reached 13.6 and 26.5% for groups A and B (P = 0.058), respectively. The durations of the procedure and postoperative hospital stay in group A were significantly shorter than those in group B (P < 0.05). Excellent follow-up results were observed in both groups. At present, no death nor major complications have occurred. Symptoms either resolved completely or improved significantly for all symptomatic infants. No residual shunts at the 6th month of follow-up evaluation were observed. Patients with failure to thrive gained weight appropriately for age, and the structure and hemodynamic parameters significantly improved during follow-up. Conclusion: Transcatheter and intraoperative device closure are feasible, effective, and safe methods for the treatment of ASDs in infants under 3 years of age. Considering improved cosmetic effect and the short duration of the procedure and postoperative hospital stay, transcatheter is preferred for patients with appropriate conditions. Intraoperative device closure can be performed as an alternative to percutaneous closure, particularly for infants with large, complex ASDs, young age, or low-body weight.